src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import jalview.analysis.AAFrequency;
  22 import jalview.analysis.AlignmentSorter;
  23 import jalview.analysis.Conservation;
  24 import jalview.analysis.CrossRef;
  25 import jalview.analysis.NJTree;
  26 import jalview.analysis.ParseProperties;
  27 import jalview.analysis.SequenceIdMatcher;
  28 import jalview.api.AlignViewControllerI;
  29 import jalview.bin.Cache;
  30 import jalview.commands.CommandI;
  31 import jalview.commands.EditCommand;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.AlignedCodonFrame;
  38 import jalview.datamodel.Alignment;
  39 import jalview.datamodel.AlignmentAnnotation;
  40 import jalview.datamodel.AlignmentI;
  41 import jalview.datamodel.AlignmentOrder;
  42 import jalview.datamodel.AlignmentView;
  43 import jalview.datamodel.ColumnSelection;
  44 import jalview.datamodel.PDBEntry;
  45 import jalview.datamodel.SeqCigar;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceGroup;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.io.AlignmentProperties;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.FeaturesFile;
  52 import jalview.io.FileLoader;
  53 import jalview.io.FormatAdapter;
  54 import jalview.io.HTMLOutput;
  55 import jalview.io.IdentifyFile;
  56 import jalview.io.JalviewFileChooser;
  57 import jalview.io.JalviewFileView;
  58 import jalview.io.JnetAnnotationMaker;
  59 import jalview.io.NewickFile;
  60 import jalview.io.TCoffeeScoreFile;
  61 import jalview.jbgui.GAlignFrame;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.ColourSchemeProperty;
  67 import jalview.schemes.HelixColourScheme;
  68 import jalview.schemes.HydrophobicColourScheme;
  69 import jalview.schemes.NucleotideColourScheme;
  70 import jalview.schemes.PIDColourScheme;
  71 import jalview.schemes.PurinePyrimidineColourScheme;
  72 import jalview.schemes.RNAHelicesColourChooser;
  73 import jalview.schemes.ResidueProperties;
  74 import jalview.schemes.StrandColourScheme;
  75 import jalview.schemes.TCoffeeColourScheme;
  76 import jalview.schemes.TaylorColourScheme;
  77 import jalview.schemes.TurnColourScheme;
  78 import jalview.schemes.UserColourScheme;
  79 import jalview.schemes.ZappoColourScheme;
  80 import jalview.util.MessageManager;
  81 import jalview.ws.jws1.Discoverer;
  82 import jalview.ws.jws2.Jws2Discoverer;
  83 import jalview.ws.jws2.jabaws2.Jws2Instance;
  84 import jalview.ws.seqfetcher.DbSourceProxy;
  85
  86 import java.awt.BorderLayout;
  87 import java.awt.Color;
  88 import java.awt.Component;
  89 import java.awt.GridLayout;
  90 import java.awt.Rectangle;
  91 import java.awt.Toolkit;
  92 import java.awt.datatransfer.Clipboard;
  93 import java.awt.datatransfer.DataFlavor;
  94 import java.awt.datatransfer.StringSelection;
  95 import java.awt.datatransfer.Transferable;
  96 import java.awt.dnd.DnDConstants;
  97 import java.awt.dnd.DropTargetDragEvent;
  98 import java.awt.dnd.DropTargetDropEvent;
  99 import java.awt.dnd.DropTargetEvent;
 100 import java.awt.dnd.DropTargetListener;
 101 import java.awt.event.ActionEvent;
 102 import java.awt.event.ActionListener;
 103 import java.awt.event.KeyAdapter;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.MouseAdapter;
 106 import java.awt.event.MouseEvent;
 107 import java.awt.print.PageFormat;
 108 import java.awt.print.PrinterJob;
 109 import java.beans.PropertyChangeEvent;
 110 import java.io.File;
 111 import java.net.URL;
 112 import java.util.ArrayList;
 113 import java.util.Enumeration;
 114 import java.util.Hashtable;
 115 import java.util.List;
 116 import java.util.Vector;
 117
 118 import javax.swing.JButton;
 119 import javax.swing.JEditorPane;
 120 import javax.swing.JInternalFrame;
 121 import javax.swing.JLabel;
 122 import javax.swing.JLayeredPane;
 123 import javax.swing.JMenu;
 124 import javax.swing.JMenuItem;
 125 import javax.swing.JOptionPane;
 126 import javax.swing.JPanel;
 127 import javax.swing.JProgressBar;
 128 import javax.swing.JRadioButtonMenuItem;
 129 import javax.swing.JScrollPane;
 130 import javax.swing.SwingUtilities;
 131
 132 /**
 133  * DOCUMENT ME!
 134  *
 135  * @author $author$
 136  * @version $Revision$
 137  */
 138 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 139         IProgressIndicator
 140 {
 141
 142   /** DOCUMENT ME!! */
 143   public static final int DEFAULT_WIDTH = 700;
 144
 145   /** DOCUMENT ME!! */
 146   public static final int DEFAULT_HEIGHT = 500;
 147
 148   public AlignmentPanel alignPanel;
 149
 150   AlignViewport viewport;
 151
 152   public AlignViewControllerI avc;
 153
 154
 155   Vector alignPanels = new Vector();
 156
 157   /**
 158    * Last format used to load or save alignments in this window
 159    */
 160   String currentFileFormat = null;
 161
 162   /**
 163    * Current filename for this alignment
 164    */
 165   String fileName = null;
 166
 167   /**
 168    * Creates a new AlignFrame object with specific width and height.
 169    *
 170    * @param al
 171    * @param width
 172    * @param height
 173    */
 174   public AlignFrame(AlignmentI al, int width, int height)
 175   {
 176     this(al, null, width, height);
 177   }
 178
 179   /**
 180    * Creates a new AlignFrame object with specific width, height and
 181    * sequenceSetId
 182    *
 183    * @param al
 184    * @param width
 185    * @param height
 186    * @param sequenceSetId
 187    */
 188   public AlignFrame(AlignmentI al, int width, int height,
 189           String sequenceSetId)
 190   {
 191     this(al, null, width, height, sequenceSetId);
 192   }
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width, height and
 196    * sequenceSetId
 197    *
 198    * @param al
 199    * @param width
 200    * @param height
 201    * @param sequenceSetId
 202    * @param viewId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId, String viewId)
 206   {
 207     this(al, null, width, height, sequenceSetId, viewId);
 208   }
 209
 210   /**
 211    * new alignment window with hidden columns
 212    *
 213    * @param al
 214    *          AlignmentI
 215    * @param hiddenColumns
 216    *          ColumnSelection or null
 217    * @param width
 218    *          Width of alignment frame
 219    * @param height
 220    *          height of frame.
 221    */
 222   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 223           int width, int height)
 224   {
 225     this(al, hiddenColumns, width, height, null);
 226   }
 227
 228   /**
 229    * Create alignment frame for al with hiddenColumns, a specific width and
 230    * height, and specific sequenceId
 231    *
 232    * @param al
 233    * @param hiddenColumns
 234    * @param width
 235    * @param height
 236    * @param sequenceSetId
 237    *          (may be null)
 238    */
 239   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 240           int width, int height, String sequenceSetId)
 241   {
 242     this(al, hiddenColumns, width, height, sequenceSetId, null);
 243   }
 244
 245   /**
 246    * Create alignment frame for al with hiddenColumns, a specific width and
 247    * height, and specific sequenceId
 248    *
 249    * @param al
 250    * @param hiddenColumns
 251    * @param width
 252    * @param height
 253    * @param sequenceSetId
 254    *          (may be null)
 255    * @param viewId
 256    *          (may be null)
 257    */
 258   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 259           int width, int height, String sequenceSetId, String viewId)
 260   {
 261     setSize(width, height);
 262     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 263
 264     alignPanel = new AlignmentPanel(this, viewport);
 265
 266     if (al.getDataset() == null)
 267     {
 268       al.setDataset(null);
 269     }
 270
 271     addAlignmentPanel(alignPanel, true);
 272     init();
 273   }
 274
 275   /**
 276    * Make a new AlignFrame from exisiting alignmentPanels
 277    *
 278    * @param ap
 279    *          AlignmentPanel
 280    * @param av
 281    *          AlignViewport
 282    */
 283   public AlignFrame(AlignmentPanel ap)
 284   {
 285     viewport = ap.av;
 286     alignPanel = ap;
 287     addAlignmentPanel(ap, false);
 288     init();
 289   }
 290
 291   /**
 292    * initalise the alignframe from the underlying viewport data and the
 293    * configurations
 294    */
 295   void init()
 296   {
 297     avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 298     if (viewport.getAlignmentConservationAnnotation() == null)
 299     {
 300       BLOSUM62Colour.setEnabled(false);
 301       conservationMenuItem.setEnabled(false);
 302       modifyConservation.setEnabled(false);
 303       // PIDColour.setEnabled(false);
 304       // abovePIDThreshold.setEnabled(false);
 305       // modifyPID.setEnabled(false);
 306     }
 307
 308     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 309             "No sort");
 310
 311     if (sortby.equals("Id"))
 312     {
 313       sortIDMenuItem_actionPerformed(null);
 314     }
 315     else if (sortby.equals("Pairwise Identity"))
 316     {
 317       sortPairwiseMenuItem_actionPerformed(null);
 318     }
 319
 320     if (Desktop.desktop != null)
 321     {
 322       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 323       addServiceListeners();
 324       setGUINucleotide(viewport.getAlignment().isNucleotide());
 325     }
 326
 327     setMenusFromViewport(viewport);
 328     buildSortByAnnotationScoresMenu();
 329     if (viewport.wrapAlignment)
 330     {
 331       wrapMenuItem_actionPerformed(null);
 332     }
 333
 334     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 335     {
 336       this.overviewMenuItem_actionPerformed(null);
 337     }
 338
 339     addKeyListener();
 340
 341   }
 342
 343   /**
 344    * Change the filename and format for the alignment, and enable the 'reload'
 345    * button functionality.
 346    *
 347    * @param file
 348    *          valid filename
 349    * @param format
 350    *          format of file
 351    */
 352   public void setFileName(String file, String format)
 353   {
 354     fileName = file;
 355     currentFileFormat = format;
 356     reload.setEnabled(true);
 357   }
 358
 359   void addKeyListener()
 360   {
 361     addKeyListener(new KeyAdapter()
 362     {
 363       @Override
 364       public void keyPressed(KeyEvent evt)
 365       {
 366         if (viewport.cursorMode
 367                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 368                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 369                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 370                 && Character.isDigit(evt.getKeyChar()))
 371           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 372
 373         switch (evt.getKeyCode())
 374         {
 375
 376         case 27: // escape key
 377           deselectAllSequenceMenuItem_actionPerformed(null);
 378
 379           break;
 380
 381         case KeyEvent.VK_DOWN:
 382           if (evt.isAltDown() || !viewport.cursorMode)
 383             moveSelectedSequences(false);
 384           if (viewport.cursorMode)
 385             alignPanel.seqPanel.moveCursor(0, 1);
 386           break;
 387
 388         case KeyEvent.VK_UP:
 389           if (evt.isAltDown() || !viewport.cursorMode)
 390             moveSelectedSequences(true);
 391           if (viewport.cursorMode)
 392             alignPanel.seqPanel.moveCursor(0, -1);
 393
 394           break;
 395
 396         case KeyEvent.VK_LEFT:
 397           if (evt.isAltDown() || !viewport.cursorMode)
 398             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 399           else
 400             alignPanel.seqPanel.moveCursor(-1, 0);
 401
 402           break;
 403
 404         case KeyEvent.VK_RIGHT:
 405           if (evt.isAltDown() || !viewport.cursorMode)
 406             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 407           else
 408             alignPanel.seqPanel.moveCursor(1, 0);
 409           break;
 410
 411         case KeyEvent.VK_SPACE:
 412           if (viewport.cursorMode)
 413           {
 414             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 415                     || evt.isShiftDown() || evt.isAltDown());
 416           }
 417           break;
 418
 419         // case KeyEvent.VK_A:
 420         // if (viewport.cursorMode)
 421         // {
 422         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 423         // //System.out.println("A");
 424         // }
 425         // break;
 426         /*
 427          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 428          * System.out.println("closing bracket"); } break;
 429          */
 430         case KeyEvent.VK_DELETE:
 431         case KeyEvent.VK_BACK_SPACE:
 432           if (!viewport.cursorMode)
 433           {
 434             cut_actionPerformed(null);
 435           }
 436           else
 437           {
 438             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 439                     || evt.isShiftDown() || evt.isAltDown());
 440           }
 441
 442           break;
 443
 444         case KeyEvent.VK_S:
 445           if (viewport.cursorMode)
 446           {
 447             alignPanel.seqPanel.setCursorRow();
 448           }
 449           break;
 450         case KeyEvent.VK_C:
 451           if (viewport.cursorMode && !evt.isControlDown())
 452           {
 453             alignPanel.seqPanel.setCursorColumn();
 454           }
 455           break;
 456         case KeyEvent.VK_P:
 457           if (viewport.cursorMode)
 458           {
 459             alignPanel.seqPanel.setCursorPosition();
 460           }
 461           break;
 462
 463         case KeyEvent.VK_ENTER:
 464         case KeyEvent.VK_COMMA:
 465           if (viewport.cursorMode)
 466           {
 467             alignPanel.seqPanel.setCursorRowAndColumn();
 468           }
 469           break;
 470
 471         case KeyEvent.VK_Q:
 472           if (viewport.cursorMode)
 473           {
 474             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 475           }
 476           break;
 477         case KeyEvent.VK_M:
 478           if (viewport.cursorMode)
 479           {
 480             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 481           }
 482           break;
 483
 484         case KeyEvent.VK_F2:
 485           viewport.cursorMode = !viewport.cursorMode;
 486           statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
 487           if (viewport.cursorMode)
 488           {
 489             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 490             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 491           }
 492           alignPanel.seqPanel.seqCanvas.repaint();
 493           break;
 494
 495         case KeyEvent.VK_F1:
 496           try
 497           {
 498             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 499             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 500                     "help/help");
 501             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 502
 503             javax.help.HelpBroker hb = hs.createHelpBroker();
 504             hb.setCurrentID("home");
 505             hb.setDisplayed(true);
 506           } catch (Exception ex)
 507           {
 508             ex.printStackTrace();
 509           }
 510           break;
 511         case KeyEvent.VK_H:
 512         {
 513           boolean toggleSeqs = !evt.isControlDown();
 514           boolean toggleCols = !evt.isShiftDown();
 515           toggleHiddenRegions(toggleSeqs, toggleCols);
 516           break;
 517         }
 518         case KeyEvent.VK_PAGE_UP:
 519           if (viewport.wrapAlignment)
 520           {
 521             alignPanel.scrollUp(true);
 522           }
 523           else
 524           {
 525             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 526                     - viewport.endSeq + viewport.startSeq);
 527           }
 528           break;
 529         case KeyEvent.VK_PAGE_DOWN:
 530           if (viewport.wrapAlignment)
 531           {
 532             alignPanel.scrollUp(false);
 533           }
 534           else
 535           {
 536             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 537                     + viewport.endSeq - viewport.startSeq);
 538           }
 539           break;
 540         }
 541       }
 542
 543       @Override
 544       public void keyReleased(KeyEvent evt)
 545       {
 546         switch (evt.getKeyCode())
 547         {
 548         case KeyEvent.VK_LEFT:
 549           if (evt.isAltDown() || !viewport.cursorMode)
 550             viewport.firePropertyChange("alignment", null, viewport
 551                     .getAlignment().getSequences());
 552           break;
 553
 554         case KeyEvent.VK_RIGHT:
 555           if (evt.isAltDown() || !viewport.cursorMode)
 556             viewport.firePropertyChange("alignment", null, viewport
 557                     .getAlignment().getSequences());
 558           break;
 559         }
 560       }
 561     });
 562   }
 563
 564   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 565   {
 566     ap.alignFrame = this;
 567     avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 568
 569     alignPanels.addElement(ap);
 570
 571     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 572
 573     int aSize = alignPanels.size();
 574
 575     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 576
 577     if (aSize == 1 && ap.av.viewName == null)
 578     {
 579       this.getContentPane().add(ap, BorderLayout.CENTER);
 580     }
 581     else
 582     {
 583       if (aSize == 2)
 584       {
 585         setInitialTabVisible();
 586       }
 587
 588       expandViews.setEnabled(true);
 589       gatherViews.setEnabled(true);
 590       tabbedPane.addTab(ap.av.viewName, ap);
 591
 592       ap.setVisible(false);
 593     }
 594
 595     if (newPanel)
 596     {
 597       if (ap.av.isPadGaps())
 598       {
 599         ap.av.getAlignment().padGaps();
 600       }
 601       ap.av.updateConservation(ap);
 602       ap.av.updateConsensus(ap);
 603       ap.av.updateStrucConsensus(ap);
 604     }
 605   }
 606
 607   public void setInitialTabVisible()
 608   {
 609     expandViews.setEnabled(true);
 610     gatherViews.setEnabled(true);
 611     tabbedPane.setVisible(true);
 612     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 613     tabbedPane.addTab(first.av.viewName, first);
 614     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 615   }
 616
 617   public AlignViewport getViewport()
 618   {
 619     return viewport;
 620   }
 621
 622   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 623   private void addServiceListeners()
 624   {
 625     final java.beans.PropertyChangeListener thisListener;
 626     Desktop.instance.addJalviewPropertyChangeListener("services",
 627             thisListener = new java.beans.PropertyChangeListener()
 628             {
 629               @Override
 630               public void propertyChange(PropertyChangeEvent evt)
 631               {
 632                 // // System.out.println("Discoverer property change.");
 633                 // if (evt.getPropertyName().equals("services"))
 634                 {
 635                   SwingUtilities.invokeLater(new Runnable()
 636                   {
 637
 638                     @Override
 639                     public void run()
 640                     {
 641                       System.err
 642                               .println("Rebuild WS Menu for service change");
 643                       BuildWebServiceMenu();
 644                     }
 645
 646                   });
 647                 }
 648               }
 649             });
 650     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 651     {
 652       @Override
 653       public void internalFrameClosed(
 654               javax.swing.event.InternalFrameEvent evt)
 655       {
 656         System.out.println("deregistering discoverer listener");
 657         Desktop.instance.removeJalviewPropertyChangeListener("services",
 658                 thisListener);
 659         closeMenuItem_actionPerformed(true);
 660       };
 661     });
 662     // Finally, build the menu once to get current service state
 663     new Thread(new Runnable()
 664     {
 665       @Override
 666       public void run()
 667       {
 668         BuildWebServiceMenu();
 669       }
 670     }).start();
 671   }
 672
 673   public void setGUINucleotide(boolean nucleotide)
 674   {
 675     showTranslation.setVisible(nucleotide);
 676     conservationMenuItem.setEnabled(!nucleotide);
 677     modifyConservation.setEnabled(!nucleotide);
 678     showGroupConservation.setEnabled(!nucleotide);
 679     rnahelicesColour.setEnabled(nucleotide);
 680     purinePyrimidineColour.setEnabled(nucleotide);
 681     // Remember AlignFrame always starts as protein
 682     // if (!nucleotide)
 683     // {
 684     // showTr
 685     // calculateMenu.remove(calculateMenu.getItemCount() - 2);
 686     // }
 687   }
 688
 689   /**
 690    * set up menus for the currently viewport. This may be called after any
 691    * operation that affects the data in the current view (selection changed,
 692    * etc) to update the menus to reflect the new state.
 693    */
 694   public void setMenusForViewport()
 695   {
 696     setMenusFromViewport(viewport);
 697   }
 698
 699   /**
 700    * Need to call this method when tabs are selected for multiple views, or when
 701    * loading from Jalview2XML.java
 702    *
 703    * @param av
 704    *          AlignViewport
 705    */
 706   void setMenusFromViewport(AlignViewport av)
 707   {
 708     padGapsMenuitem.setSelected(av.isPadGaps());
 709     colourTextMenuItem.setSelected(av.showColourText);
 710     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 711     conservationMenuItem.setSelected(av.getConservationSelected());
 712     seqLimits.setSelected(av.getShowJVSuffix());
 713     idRightAlign.setSelected(av.rightAlignIds);
 714     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 715     renderGapsMenuItem.setSelected(av.renderGaps);
 716     wrapMenuItem.setSelected(av.wrapAlignment);
 717     scaleAbove.setVisible(av.wrapAlignment);
 718     scaleLeft.setVisible(av.wrapAlignment);
 719     scaleRight.setVisible(av.wrapAlignment);
 720     annotationPanelMenuItem.setState(av.showAnnotation);
 721     viewBoxesMenuItem.setSelected(av.showBoxes);
 722     viewTextMenuItem.setSelected(av.showText);
 723     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 724     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 725     showGroupConservation.setSelected(av.isShowGroupConservation());
 726     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 727     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 728     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 729
 730     setColourSelected(ColourSchemeProperty.getColourName(av
 731             .getGlobalColourScheme()));
 732
 733     showSeqFeatures.setSelected(av.showSequenceFeatures);
 734     hiddenMarkers.setState(av.showHiddenMarkers);
 735     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 736     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 737     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 738     autoCalculate.setSelected(av.autoCalculateConsensus);
 739     sortByTree.setSelected(av.sortByTree);
 740     listenToViewSelections.setSelected(av.followSelection);
 741     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 742     rnahelicesColour
 743             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 744     setShowProductsEnabled();
 745     updateEditMenuBar();
 746   }
 747
 748   // methods for implementing IProgressIndicator
 749   // need to refactor to a reusable stub class
 750   Hashtable progressBars, progressBarHandlers;
 751
 752   /*
 753    * (non-Javadoc)
 754    *
 755    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 756    */
 757   @Override
 758   public void setProgressBar(String message, long id)
 759   {
 760     if (progressBars == null)
 761     {
 762       progressBars = new Hashtable();
 763       progressBarHandlers = new Hashtable();
 764     }
 765
 766     JPanel progressPanel;
 767     Long lId = new Long(id);
 768     GridLayout layout = (GridLayout) statusPanel.getLayout();
 769     if (progressBars.get(lId) != null)
 770     {
 771       progressPanel = (JPanel) progressBars.get(new Long(id));
 772       statusPanel.remove(progressPanel);
 773       progressBars.remove(lId);
 774       progressPanel = null;
 775       if (message != null)
 776       {
 777         statusBar.setText(message);
 778       }
 779       if (progressBarHandlers.contains(lId))
 780       {
 781         progressBarHandlers.remove(lId);
 782       }
 783       layout.setRows(layout.getRows() - 1);
 784     }
 785     else
 786     {
 787       progressPanel = new JPanel(new BorderLayout(10, 5));
 788
 789       JProgressBar progressBar = new JProgressBar();
 790       progressBar.setIndeterminate(true);
 791
 792       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 793       progressPanel.add(progressBar, BorderLayout.CENTER);
 794
 795       layout.setRows(layout.getRows() + 1);
 796       statusPanel.add(progressPanel);
 797
 798       progressBars.put(lId, progressPanel);
 799     }
 800     // update GUI
 801     // setMenusForViewport();
 802     validate();
 803   }
 804
 805   @Override
 806   public void registerHandler(final long id,
 807           final IProgressIndicatorHandler handler)
 808   {
 809     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 810     {
 811       throw new Error(
 812               "call setProgressBar before registering the progress bar's handler.");
 813     }
 814     progressBarHandlers.put(new Long(id), handler);
 815     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 816     if (handler.canCancel())
 817     {
 818       JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 819       final IProgressIndicator us = this;
 820       cancel.addActionListener(new ActionListener()
 821       {
 822
 823         @Override
 824         public void actionPerformed(ActionEvent e)
 825         {
 826           handler.cancelActivity(id);
 827           us.setProgressBar(
 828                   "Cancelled "
 829                           + ((JLabel) progressPanel.getComponent(0))
 830                                   .getText(), id);
 831         }
 832       });
 833       progressPanel.add(cancel, BorderLayout.EAST);
 834     }
 835   }
 836
 837   /**
 838    *
 839    * @return true if any progress bars are still active
 840    */
 841   @Override
 842   public boolean operationInProgress()
 843   {
 844     if (progressBars != null && progressBars.size() > 0)
 845     {
 846       return true;
 847     }
 848     return false;
 849   }
 850
 851   /*
 852    * Added so Castor Mapping file can obtain Jalview Version
 853    */
 854   public String getVersion()
 855   {
 856     return jalview.bin.Cache.getProperty("VERSION");
 857   }
 858
 859   public FeatureRenderer getFeatureRenderer()
 860   {
 861     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 862   }
 863
 864   @Override
 865   public void fetchSequence_actionPerformed(ActionEvent e)
 866   {
 867     new SequenceFetcher(this);
 868   }
 869
 870   @Override
 871   public void addFromFile_actionPerformed(ActionEvent e)
 872   {
 873     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 874   }
 875
 876   @Override
 877   public void reload_actionPerformed(ActionEvent e)
 878   {
 879     if (fileName != null)
 880     {
 881       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 882       // originating file's format
 883       // TODO: work out how to recover feature settings for correct view(s) when
 884       // file is reloaded.
 885       if (currentFileFormat.equals("Jalview"))
 886       {
 887         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 888         for (int i = 0; i < frames.length; i++)
 889         {
 890           if (frames[i] instanceof AlignFrame && frames[i] != this
 891                   && ((AlignFrame) frames[i]).fileName != null
 892                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 893           {
 894             try
 895             {
 896               frames[i].setSelected(true);
 897               Desktop.instance.closeAssociatedWindows();
 898             } catch (java.beans.PropertyVetoException ex)
 899             {
 900             }
 901           }
 902
 903         }
 904         Desktop.instance.closeAssociatedWindows();
 905
 906         FileLoader loader = new FileLoader();
 907         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 908         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 909       }
 910       else
 911       {
 912         Rectangle bounds = this.getBounds();
 913
 914         FileLoader loader = new FileLoader();
 915         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 916         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 917                 protocol, currentFileFormat);
 918
 919         newframe.setBounds(bounds);
 920         if (featureSettings != null && featureSettings.isShowing())
 921         {
 922           final Rectangle fspos = featureSettings.frame.getBounds();
 923           // TODO: need a 'show feature settings' function that takes bounds -
 924           // need to refactor Desktop.addFrame
 925           newframe.featureSettings_actionPerformed(null);
 926           final FeatureSettings nfs = newframe.featureSettings;
 927           SwingUtilities.invokeLater(new Runnable()
 928           {
 929             @Override
 930             public void run()
 931             {
 932               nfs.frame.setBounds(fspos);
 933             }
 934           });
 935           this.featureSettings.close();
 936           this.featureSettings = null;
 937         }
 938         this.closeMenuItem_actionPerformed(true);
 939       }
 940     }
 941   }
 942
 943   @Override
 944   public void addFromText_actionPerformed(ActionEvent e)
 945   {
 946     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 947   }
 948
 949   @Override
 950   public void addFromURL_actionPerformed(ActionEvent e)
 951   {
 952     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 953   }
 954
 955   @Override
 956   public void save_actionPerformed(ActionEvent e)
 957   {
 958     if (fileName == null
 959             || (currentFileFormat == null || !jalview.io.FormatAdapter
 960                     .isValidIOFormat(currentFileFormat, true))
 961             || fileName.startsWith("http"))
 962     {
 963       saveAs_actionPerformed(null);
 964     }
 965     else
 966     {
 967       saveAlignment(fileName, currentFileFormat);
 968     }
 969   }
 970
 971   /**
 972    * DOCUMENT ME!
 973    *
 974    * @param e
 975    *          DOCUMENT ME!
 976    */
 977   @Override
 978   public void saveAs_actionPerformed(ActionEvent e)
 979   {
 980     JalviewFileChooser chooser = new JalviewFileChooser(
 981             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 982             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 983             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 984             currentFileFormat, false);
 985
 986     chooser.setFileView(new JalviewFileView());
 987     chooser.setDialogTitle("Save Alignment to file");
 988     chooser.setToolTipText(MessageManager.getString("action.save"));\r
 989
 990     int value = chooser.showSaveDialog(this);
 991
 992     if (value == JalviewFileChooser.APPROVE_OPTION)
 993     {
 994       currentFileFormat = chooser.getSelectedFormat();
 995       if (currentFileFormat == null)
 996       {
 997         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 998                 MessageManager.getString("label.select_file_format_before_saving"),
 999                 MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
1000         value = chooser.showSaveDialog(this);
1001         return;
1002       }
1003
1004       fileName = chooser.getSelectedFile().getPath();
1005
1006       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1007               currentFileFormat);
1008
1009       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1010       if (currentFileFormat.indexOf(" ") > -1)
1011       {
1012         currentFileFormat = currentFileFormat.substring(0,
1013                 currentFileFormat.indexOf(" "));
1014       }
1015       saveAlignment(fileName, currentFileFormat);
1016     }
1017   }
1018
1019   public boolean saveAlignment(String file, String format)
1020   {
1021     boolean success = true;
1022
1023     if (format.equalsIgnoreCase("Jalview"))
1024     {
1025       String shortName = title;
1026
1027       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1028       {
1029         shortName = shortName.substring(shortName
1030                 .lastIndexOf(java.io.File.separatorChar) + 1);
1031       }
1032
1033       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1034
1035       statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1036
1037
1038     }
1039     else
1040     {
1041       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1042       {
1043         warningMessage("Cannot save file " + fileName + " using format "
1044                 + format, "Alignment output format not supported");
1045         saveAs_actionPerformed(null);
1046         // JBPNote need to have a raise_gui flag here
1047         return false;
1048       }
1049
1050       String[] omitHidden = null;
1051
1052       if (viewport.hasHiddenColumns())
1053       {
1054         int reply = JOptionPane
1055                 .showInternalConfirmDialog(
1056                         Desktop.desktop,
1057                         MessageManager.getString("label.alignment_contains_hidden_columns"),
1058                         MessageManager.getString("action.save_omit_hidden_columns"),
1059                         JOptionPane.YES_NO_OPTION,
1060                         JOptionPane.QUESTION_MESSAGE);
1061
1062         if (reply == JOptionPane.YES_OPTION)
1063         {
1064           omitHidden = viewport.getViewAsString(false);
1065         }
1066       }
1067       FormatAdapter f = new FormatAdapter();
1068       String output = f.formatSequences(format,
1069               viewport.getAlignment(), // class cast exceptions will
1070               // occur in the distant future
1071               omitHidden, f.getCacheSuffixDefault(format),
1072               viewport.getColumnSelection());
1073
1074       if (output == null)
1075       {
1076         success = false;
1077       }
1078       else
1079       {
1080         try
1081         {
1082           java.io.PrintWriter out = new java.io.PrintWriter(
1083                   new java.io.FileWriter(file));
1084
1085           out.print(output);
1086           out.close();
1087           this.setTitle(file);
1088           statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1089         } catch (Exception ex)
1090         {
1091           success = false;
1092           ex.printStackTrace();
1093         }
1094       }
1095     }
1096
1097     if (!success)
1098     {
1099       JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
1100               MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
1101     }
1102
1103     return success;
1104   }
1105
1106   private void warningMessage(String warning, String title)
1107   {
1108     if (new jalview.util.Platform().isHeadless())
1109     {
1110       System.err.println("Warning: " + title + "\nWarning: " + warning);
1111
1112     }
1113     else
1114     {
1115       JOptionPane.showInternalMessageDialog(this, warning, title,
1116               JOptionPane.WARNING_MESSAGE);
1117     }
1118     return;
1119   }
1120
1121   /**
1122    * DOCUMENT ME!
1123    *
1124    * @param e
1125    *          DOCUMENT ME!
1126    */
1127   @Override
1128   protected void outputText_actionPerformed(ActionEvent e)
1129   {
1130     String[] omitHidden = null;
1131
1132     if (viewport.hasHiddenColumns())
1133     {
1134       int reply = JOptionPane
1135               .showInternalConfirmDialog(
1136                       Desktop.desktop,
1137                       MessageManager.getString("label.alignment_contains_hidden_columns"),
1138                       MessageManager.getString("action.save_omit_hidden_columns"),
1139                       JOptionPane.YES_NO_OPTION,
1140                       JOptionPane.QUESTION_MESSAGE);
1141
1142       if (reply == JOptionPane.YES_OPTION)
1143       {
1144         omitHidden = viewport.getViewAsString(false);
1145       }
1146     }
1147
1148     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1149     cap.setForInput(null);
1150
1151     try
1152     {
1153       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1154               viewport.getAlignment(), omitHidden,
1155               viewport.getColumnSelection()));
1156       Desktop.addInternalFrame(cap,
1157               MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
1158     } catch (OutOfMemoryError oom)
1159     {
1160       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1161       cap.dispose();
1162     }
1163
1164   }
1165
1166   /**
1167    * DOCUMENT ME!
1168    *
1169    * @param e
1170    *          DOCUMENT ME!
1171    */
1172   @Override
1173   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1174   {
1175     new HTMLOutput(alignPanel,
1176             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1177             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1178   }
1179
1180   public void createImageMap(File file, String image)
1181   {
1182     alignPanel.makePNGImageMap(file, image);
1183   }
1184
1185   /**
1186    * DOCUMENT ME!
1187    *
1188    * @param e
1189    *          DOCUMENT ME!
1190    */
1191   @Override
1192   public void createPNG(File f)
1193   {
1194     alignPanel.makePNG(f);
1195   }
1196
1197   /**
1198    * DOCUMENT ME!
1199    *
1200    * @param e
1201    *          DOCUMENT ME!
1202    */
1203   @Override
1204   public void createEPS(File f)
1205   {
1206     alignPanel.makeEPS(f);
1207   }
1208
1209   @Override
1210   public void pageSetup_actionPerformed(ActionEvent e)
1211   {
1212     PrinterJob printJob = PrinterJob.getPrinterJob();
1213     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1214   }
1215
1216   /**
1217    * DOCUMENT ME!
1218    *
1219    * @param e
1220    *          DOCUMENT ME!
1221    */
1222   @Override
1223   public void printMenuItem_actionPerformed(ActionEvent e)
1224   {
1225     // Putting in a thread avoids Swing painting problems
1226     PrintThread thread = new PrintThread(alignPanel);
1227     thread.start();
1228   }
1229
1230   @Override
1231   public void exportFeatures_actionPerformed(ActionEvent e)
1232   {
1233     new AnnotationExporter().exportFeatures(alignPanel);
1234   }
1235
1236   @Override
1237   public void exportAnnotations_actionPerformed(ActionEvent e)
1238   {
1239     new AnnotationExporter().exportAnnotations(alignPanel,
1240             viewport.showAnnotation ? viewport.getAlignment()
1241                     .getAlignmentAnnotation() : null, viewport
1242                     .getAlignment().getGroups(), ((Alignment) viewport
1243                     .getAlignment()).alignmentProperties);
1244   }
1245
1246   @Override
1247   public void associatedData_actionPerformed(ActionEvent e)
1248   {
1249     // Pick the tree file
1250     JalviewFileChooser chooser = new JalviewFileChooser(
1251             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1252     chooser.setFileView(new JalviewFileView());
1253     chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
1254     chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
1255
1256     int value = chooser.showOpenDialog(null);
1257
1258     if (value == JalviewFileChooser.APPROVE_OPTION)
1259     {
1260       String choice = chooser.getSelectedFile().getPath();
1261       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1262       loadJalviewDataFile(choice, null, null, null);
1263     }
1264
1265   }
1266
1267   /**
1268    * Close the current view or all views in the alignment frame. If the frame
1269    * only contains one view then the alignment will be removed from memory.
1270    *
1271    * @param closeAllTabs
1272    */
1273   @Override
1274   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1275   {
1276     if (alignPanels != null && alignPanels.size() < 2)
1277     {
1278       closeAllTabs = true;
1279     }
1280
1281     try
1282     {
1283       if (alignPanels != null)
1284       {
1285         if (closeAllTabs)
1286         {
1287           if (this.isClosed())
1288           {
1289             // really close all the windows - otherwise wait till
1290             // setClosed(true) is called
1291             for (int i = 0; i < alignPanels.size(); i++)
1292             {
1293               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1294               ap.closePanel();
1295             }
1296           }
1297         }
1298         else
1299         {
1300           closeView(alignPanel);
1301         }
1302       }
1303
1304       if (closeAllTabs)
1305       {
1306         this.setClosed(true);
1307       }
1308     } catch (Exception ex)
1309     {
1310       ex.printStackTrace();
1311     }
1312   }
1313
1314   /**
1315    * close alignPanel2 and shuffle tabs appropriately.
1316    *
1317    * @param alignPanel2
1318    */
1319   public void closeView(AlignmentPanel alignPanel2)
1320   {
1321     int index = tabbedPane.getSelectedIndex();
1322     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1323     alignPanels.removeElement(alignPanel2);
1324     // Unnecessary
1325     // if (viewport == alignPanel2.av)
1326     // {
1327     // viewport = null;
1328     // }
1329     alignPanel2.closePanel();
1330     alignPanel2 = null;
1331
1332     tabbedPane.removeTabAt(closedindex);
1333     tabbedPane.validate();
1334
1335     if (index > closedindex || index == tabbedPane.getTabCount())
1336     {
1337       // modify currently selected tab index if necessary.
1338       index--;
1339     }
1340
1341     this.tabSelectionChanged(index);
1342   }
1343
1344   /**
1345    * DOCUMENT ME!
1346    */
1347   void updateEditMenuBar()
1348   {
1349
1350     if (viewport.historyList.size() > 0)
1351     {
1352       undoMenuItem.setEnabled(true);
1353       CommandI command = (CommandI) viewport.historyList.peek();
1354       undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1355     }
1356     else
1357     {
1358       undoMenuItem.setEnabled(false);
1359       undoMenuItem.setText(MessageManager.getString("action.undo"));
1360     }
1361
1362     if (viewport.redoList.size() > 0)
1363     {
1364       redoMenuItem.setEnabled(true);
1365
1366       CommandI command = (CommandI) viewport.redoList.peek();
1367       redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1368     }
1369     else
1370     {
1371       redoMenuItem.setEnabled(false);
1372       redoMenuItem.setText(MessageManager.getString("action.redo"));
1373     }
1374   }
1375
1376   public void addHistoryItem(CommandI command)
1377   {
1378     if (command.getSize() > 0)
1379     {
1380       viewport.historyList.push(command);
1381       viewport.redoList.clear();
1382       updateEditMenuBar();
1383       viewport.updateHiddenColumns();
1384       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1385       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1386       // viewport.getColumnSelection()
1387       // .getHiddenColumns().size() > 0);
1388     }
1389   }
1390
1391   /**
1392    *
1393    * @return alignment objects for all views
1394    */
1395   AlignmentI[] getViewAlignments()
1396   {
1397     if (alignPanels != null)
1398     {
1399       Enumeration e = alignPanels.elements();
1400       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1401       for (int i = 0; e.hasMoreElements(); i++)
1402       {
1403         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1404       }
1405       return als;
1406     }
1407     if (viewport != null)
1408     {
1409       return new AlignmentI[]
1410       { viewport.getAlignment() };
1411     }
1412     return null;
1413   }
1414
1415   /**
1416    * DOCUMENT ME!
1417    *
1418    * @param e
1419    *          DOCUMENT ME!
1420    */
1421   @Override
1422   protected void undoMenuItem_actionPerformed(ActionEvent e)
1423   {
1424     if (viewport.historyList.empty())
1425       return;
1426     CommandI command = (CommandI) viewport.historyList.pop();
1427     viewport.redoList.push(command);
1428     command.undoCommand(getViewAlignments());
1429
1430     AlignViewport originalSource = getOriginatingSource(command);
1431     updateEditMenuBar();
1432
1433     if (originalSource != null)
1434     {
1435       if (originalSource != viewport)
1436       {
1437         Cache.log
1438                 .warn("Implementation worry: mismatch of viewport origin for undo");
1439       }
1440       originalSource.updateHiddenColumns();
1441       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1442       // null
1443       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1444       // viewport.getColumnSelection()
1445       // .getHiddenColumns().size() > 0);
1446       originalSource.firePropertyChange("alignment", null, originalSource
1447               .getAlignment().getSequences());
1448     }
1449   }
1450
1451   /**
1452    * DOCUMENT ME!
1453    *
1454    * @param e
1455    *          DOCUMENT ME!
1456    */
1457   @Override
1458   protected void redoMenuItem_actionPerformed(ActionEvent e)
1459   {
1460     if (viewport.redoList.size() < 1)
1461     {
1462       return;
1463     }
1464
1465     CommandI command = (CommandI) viewport.redoList.pop();
1466     viewport.historyList.push(command);
1467     command.doCommand(getViewAlignments());
1468
1469     AlignViewport originalSource = getOriginatingSource(command);
1470     updateEditMenuBar();
1471
1472     if (originalSource != null)
1473     {
1474
1475       if (originalSource != viewport)
1476       {
1477         Cache.log
1478                 .warn("Implementation worry: mismatch of viewport origin for redo");
1479       }
1480       originalSource.updateHiddenColumns();
1481       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1482       // null
1483       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1484       // viewport.getColumnSelection()
1485       // .getHiddenColumns().size() > 0);
1486       originalSource.firePropertyChange("alignment", null, originalSource
1487               .getAlignment().getSequences());
1488     }
1489   }
1490
1491   AlignViewport getOriginatingSource(CommandI command)
1492   {
1493     AlignViewport originalSource = null;
1494     // For sequence removal and addition, we need to fire
1495     // the property change event FROM the viewport where the
1496     // original alignment was altered
1497     AlignmentI al = null;
1498     if (command instanceof EditCommand)
1499     {
1500       EditCommand editCommand = (EditCommand) command;
1501       al = editCommand.getAlignment();
1502       Vector comps = (Vector) PaintRefresher.components.get(viewport
1503               .getSequenceSetId());
1504
1505       for (int i = 0; i < comps.size(); i++)
1506       {
1507         if (comps.elementAt(i) instanceof AlignmentPanel)
1508         {
1509           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1510           {
1511             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1512             break;
1513           }
1514         }
1515       }
1516     }
1517
1518     if (originalSource == null)
1519     {
1520       // The original view is closed, we must validate
1521       // the current view against the closed view first
1522       if (al != null)
1523       {
1524         PaintRefresher.validateSequences(al, viewport.getAlignment());
1525       }
1526
1527       originalSource = viewport;
1528     }
1529
1530     return originalSource;
1531   }
1532
1533   /**
1534    * DOCUMENT ME!
1535    *
1536    * @param up
1537    *          DOCUMENT ME!
1538    */
1539   public void moveSelectedSequences(boolean up)
1540   {
1541     SequenceGroup sg = viewport.getSelectionGroup();
1542
1543     if (sg == null)
1544     {
1545       return;
1546     }
1547     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1548             viewport.getHiddenRepSequences(), up);
1549     alignPanel.paintAlignment(true);
1550   }
1551
1552   synchronized void slideSequences(boolean right, int size)
1553   {
1554     List<SequenceI> sg = new Vector();
1555     if (viewport.cursorMode)
1556     {
1557       sg.add(viewport.getAlignment().getSequenceAt(
1558               alignPanel.seqPanel.seqCanvas.cursorY));
1559     }
1560     else if (viewport.getSelectionGroup() != null
1561             && viewport.getSelectionGroup().getSize() != viewport
1562                     .getAlignment().getHeight())
1563     {
1564       sg = viewport.getSelectionGroup().getSequences(
1565               viewport.getHiddenRepSequences());
1566     }
1567
1568     if (sg.size() < 1)
1569     {
1570       return;
1571     }
1572
1573     Vector invertGroup = new Vector();
1574
1575     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1576     {
1577       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1578         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1579     }
1580
1581     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1582
1583     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1584     for (int i = 0; i < invertGroup.size(); i++)
1585       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1586
1587     SlideSequencesCommand ssc;
1588     if (right)
1589       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1590               size, viewport.getGapCharacter());
1591     else
1592       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1593               size, viewport.getGapCharacter());
1594
1595     int groupAdjustment = 0;
1596     if (ssc.getGapsInsertedBegin() && right)
1597     {
1598       if (viewport.cursorMode)
1599         alignPanel.seqPanel.moveCursor(size, 0);
1600       else
1601         groupAdjustment = size;
1602     }
1603     else if (!ssc.getGapsInsertedBegin() && !right)
1604     {
1605       if (viewport.cursorMode)
1606         alignPanel.seqPanel.moveCursor(-size, 0);
1607       else
1608         groupAdjustment = -size;
1609     }
1610
1611     if (groupAdjustment != 0)
1612     {
1613       viewport.getSelectionGroup().setStartRes(
1614               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1615       viewport.getSelectionGroup().setEndRes(
1616               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1617     }
1618
1619     boolean appendHistoryItem = false;
1620     if (viewport.historyList != null && viewport.historyList.size() > 0
1621             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1622     {
1623       appendHistoryItem = ssc
1624               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1625                       .peek());
1626     }
1627
1628     if (!appendHistoryItem)
1629       addHistoryItem(ssc);
1630
1631     repaint();
1632   }
1633
1634   /**
1635    * DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   @Override
1641   protected void copy_actionPerformed(ActionEvent e)
1642   {
1643     System.gc();
1644     if (viewport.getSelectionGroup() == null)
1645     {
1646       return;
1647     }
1648     // TODO: preserve the ordering of displayed alignment annotation in any
1649     // internal paste (particularly sequence associated annotation)
1650     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1651     String[] omitHidden = null;
1652
1653     if (viewport.hasHiddenColumns())
1654     {
1655       omitHidden = viewport.getViewAsString(true);
1656     }
1657
1658     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1659             omitHidden);
1660
1661     StringSelection ss = new StringSelection(output);
1662
1663     try
1664     {
1665       jalview.gui.Desktop.internalCopy = true;
1666       // Its really worth setting the clipboard contents
1667       // to empty before setting the large StringSelection!!
1668       Toolkit.getDefaultToolkit().getSystemClipboard()
1669               .setContents(new StringSelection(""), null);
1670
1671       Toolkit.getDefaultToolkit().getSystemClipboard()
1672               .setContents(ss, Desktop.instance);
1673     } catch (OutOfMemoryError er)
1674     {
1675       new OOMWarning("copying region", er);
1676       return;
1677     }
1678
1679     Vector hiddenColumns = null;
1680     if (viewport.hasHiddenColumns())
1681     {
1682       hiddenColumns = new Vector();
1683       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1684               .getSelectionGroup().getEndRes();
1685       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1686               .size(); i++)
1687       {
1688         int[] region = (int[]) viewport.getColumnSelection()
1689                 .getHiddenColumns().elementAt(i);
1690         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1691         {
1692           hiddenColumns.addElement(new int[]
1693           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1694         }
1695       }
1696     }
1697
1698     Desktop.jalviewClipboard = new Object[]
1699     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1700     statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
1701   }
1702
1703   /**
1704    * DOCUMENT ME!
1705    *
1706    * @param e
1707    *          DOCUMENT ME!
1708    */
1709   @Override
1710   protected void pasteNew_actionPerformed(ActionEvent e)
1711   {
1712     paste(true);
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param e
1719    *          DOCUMENT ME!
1720    */
1721   @Override
1722   protected void pasteThis_actionPerformed(ActionEvent e)
1723   {
1724     paste(false);
1725   }
1726
1727   /**
1728    * Paste contents of Jalview clipboard
1729    *
1730    * @param newAlignment
1731    *          true to paste to a new alignment, otherwise add to this.
1732    */
1733   void paste(boolean newAlignment)
1734   {
1735     boolean externalPaste = true;
1736     try
1737     {
1738       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1739       Transferable contents = c.getContents(this);
1740
1741       if (contents == null)
1742       {
1743         return;
1744       }
1745
1746       String str, format;
1747       try
1748       {
1749         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1750         if (str.length() < 1)
1751         {
1752           return;
1753         }
1754
1755         format = new IdentifyFile().Identify(str, "Paste");
1756
1757       } catch (OutOfMemoryError er)
1758       {
1759         new OOMWarning("Out of memory pasting sequences!!", er);
1760         return;
1761       }
1762
1763       SequenceI[] sequences;
1764       boolean annotationAdded = false;
1765       AlignmentI alignment = null;
1766
1767       if (Desktop.jalviewClipboard != null)
1768       {
1769         // The clipboard was filled from within Jalview, we must use the
1770         // sequences
1771         // And dataset from the copied alignment
1772         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1773         // be doubly sure that we create *new* sequence objects.
1774         sequences = new SequenceI[newseq.length];
1775         for (int i = 0; i < newseq.length; i++)
1776         {
1777           sequences[i] = new Sequence(newseq[i]);
1778         }
1779         alignment = new Alignment(sequences);
1780         externalPaste = false;
1781       }
1782       else
1783       {
1784         // parse the clipboard as an alignment.
1785         alignment = new FormatAdapter().readFile(str, "Paste", format);
1786         sequences = alignment.getSequencesArray();
1787       }
1788
1789       int alwidth = 0;
1790       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1791       int fgroup = -1;
1792
1793       if (newAlignment)
1794       {
1795
1796         if (Desktop.jalviewClipboard != null)
1797         {
1798           // dataset is inherited
1799           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1800         }
1801         else
1802         {
1803           // new dataset is constructed
1804           alignment.setDataset(null);
1805         }
1806         alwidth = alignment.getWidth() + 1;
1807       }
1808       else
1809       {
1810         AlignmentI pastedal = alignment; // preserve pasted alignment object
1811         // Add pasted sequences and dataset into existing alignment.
1812         alignment = viewport.getAlignment();
1813         alwidth = alignment.getWidth() + 1;
1814         // decide if we need to import sequences from an existing dataset
1815         boolean importDs = Desktop.jalviewClipboard != null
1816                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1817         // importDs==true instructs us to copy over new dataset sequences from
1818         // an existing alignment
1819         Vector newDs = (importDs) ? new Vector() : null; // used to create
1820         // minimum dataset set
1821
1822         for (int i = 0; i < sequences.length; i++)
1823         {
1824           if (importDs)
1825           {
1826             newDs.addElement(null);
1827           }
1828           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1829           // paste
1830           if (importDs && ds != null)
1831           {
1832             if (!newDs.contains(ds))
1833             {
1834               newDs.setElementAt(ds, i);
1835               ds = new Sequence(ds);
1836               // update with new dataset sequence
1837               sequences[i].setDatasetSequence(ds);
1838             }
1839             else
1840             {
1841               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1842             }
1843           }
1844           else
1845           {
1846             // copy and derive new dataset sequence
1847             sequences[i] = sequences[i].deriveSequence();
1848             alignment.getDataset().addSequence(
1849                     sequences[i].getDatasetSequence());
1850             // TODO: avoid creation of duplicate dataset sequences with a
1851             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1852           }
1853           alignment.addSequence(sequences[i]); // merges dataset
1854         }
1855         if (newDs != null)
1856         {
1857           newDs.clear(); // tidy up
1858         }
1859         if (alignment.getAlignmentAnnotation() != null)
1860         {
1861           for (AlignmentAnnotation alan : alignment
1862                   .getAlignmentAnnotation())
1863           {
1864             if (alan.graphGroup > fgroup)
1865             {
1866               fgroup = alan.graphGroup;
1867             }
1868           }
1869         }
1870         if (pastedal.getAlignmentAnnotation() != null)
1871         {
1872           // Add any annotation attached to alignment.
1873           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1874           for (int i = 0; i < alann.length; i++)
1875           {
1876             annotationAdded = true;
1877             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1878             {
1879               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1880               if (newann.graphGroup > -1)
1881               {
1882                 if (newGraphGroups.size() <= newann.graphGroup
1883                         || newGraphGroups.get(newann.graphGroup) == null)
1884                 {
1885                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1886                   {
1887                     newGraphGroups.add(q, null);
1888                   }
1889                   newGraphGroups.set(newann.graphGroup, new Integer(
1890                           ++fgroup));
1891                 }
1892                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1893                         .intValue();
1894               }
1895
1896               newann.padAnnotation(alwidth);
1897               alignment.addAnnotation(newann);
1898             }
1899           }
1900         }
1901       }
1902       if (!newAlignment)
1903       {
1904         // /////
1905         // ADD HISTORY ITEM
1906         //
1907         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1908                 sequences, 0, alignment.getWidth(), alignment));
1909       }
1910       // Add any annotations attached to sequences
1911       for (int i = 0; i < sequences.length; i++)
1912       {
1913         if (sequences[i].getAnnotation() != null)
1914         {
1915           AlignmentAnnotation newann;
1916           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1917           {
1918             annotationAdded = true;
1919             newann = sequences[i].getAnnotation()[a];
1920             newann.adjustForAlignment();
1921             newann.padAnnotation(alwidth);
1922             if (newann.graphGroup > -1)
1923             {
1924               if (newann.graphGroup > -1)
1925               {
1926                 if (newGraphGroups.size() <= newann.graphGroup
1927                         || newGraphGroups.get(newann.graphGroup) == null)
1928                 {
1929                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1930                   {
1931                     newGraphGroups.add(q, null);
1932                   }
1933                   newGraphGroups.set(newann.graphGroup, new Integer(
1934                           ++fgroup));
1935                 }
1936                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1937                         .intValue();
1938               }
1939             }
1940             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1941             // was
1942             // duplicated
1943             // earlier
1944             alignment
1945                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1946           }
1947         }
1948       }
1949       if (!newAlignment)
1950       {
1951
1952         // propagate alignment changed.
1953         viewport.setEndSeq(alignment.getHeight());
1954         if (annotationAdded)
1955         {
1956           // Duplicate sequence annotation in all views.
1957           AlignmentI[] alview = this.getViewAlignments();
1958           for (int i = 0; i < sequences.length; i++)
1959           {
1960             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1961             if (sann == null)
1962               continue;
1963             for (int avnum = 0; avnum < alview.length; avnum++)
1964             {
1965               if (alview[avnum] != alignment)
1966               {
1967                 // duplicate in a view other than the one with input focus
1968                 int avwidth = alview[avnum].getWidth() + 1;
1969                 // this relies on sann being preserved after we
1970                 // modify the sequence's annotation array for each duplication
1971                 for (int a = 0; a < sann.length; a++)
1972                 {
1973                   AlignmentAnnotation newann = new AlignmentAnnotation(
1974                           sann[a]);
1975                   sequences[i].addAlignmentAnnotation(newann);
1976                   newann.padAnnotation(avwidth);
1977                   alview[avnum].addAnnotation(newann); // annotation was
1978                   // duplicated earlier
1979                   // TODO JAL-1145 graphGroups are not updated for sequence
1980                   // annotation added to several views. This may cause
1981                   // strangeness
1982                   alview[avnum].setAnnotationIndex(newann, a);
1983                 }
1984               }
1985             }
1986           }
1987           buildSortByAnnotationScoresMenu();
1988         }
1989         viewport.firePropertyChange("alignment", null,
1990                 alignment.getSequences());
1991         if (alignPanels != null)
1992         {
1993           for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
1994           {
1995             ap.validateAnnotationDimensions(false);
1996           }
1997         }
1998         else
1999         {
2000           alignPanel.validateAnnotationDimensions(false);
2001         }
2002
2003       }
2004       else
2005       {
2006         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2007                 DEFAULT_HEIGHT);
2008         String newtitle = new String("Copied sequences");
2009
2010         if (Desktop.jalviewClipboard != null
2011                 && Desktop.jalviewClipboard[2] != null)
2012         {
2013           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2014           for (int i = 0; i < hc.size(); i++)
2015           {
2016             int[] region = (int[]) hc.elementAt(i);
2017             af.viewport.hideColumns(region[0], region[1]);
2018           }
2019         }
2020
2021         // >>>This is a fix for the moment, until a better solution is
2022         // found!!<<<
2023         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2024                 .transferSettings(
2025                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2026
2027         // TODO: maintain provenance of an alignment, rather than just make the
2028         // title a concatenation of operations.
2029         if (!externalPaste)
2030         {
2031           if (title.startsWith("Copied sequences"))
2032           {
2033             newtitle = title;
2034           }
2035           else
2036           {
2037             newtitle = newtitle.concat("- from " + title);
2038           }
2039         }
2040         else
2041         {
2042           newtitle = new String("Pasted sequences");
2043         }
2044
2045         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2046                 DEFAULT_HEIGHT);
2047
2048       }
2049
2050     } catch (Exception ex)
2051     {
2052       ex.printStackTrace();
2053       System.out.println("Exception whilst pasting: " + ex);
2054       // could be anything being pasted in here
2055     }
2056
2057   }
2058
2059   /**
2060    * DOCUMENT ME!
2061    *
2062    * @param e
2063    *          DOCUMENT ME!
2064    */
2065   @Override
2066   protected void cut_actionPerformed(ActionEvent e)
2067   {
2068     copy_actionPerformed(null);
2069     delete_actionPerformed(null);
2070   }
2071
2072   /**
2073    * DOCUMENT ME!
2074    *
2075    * @param e
2076    *          DOCUMENT ME!
2077    */
2078   @Override
2079   protected void delete_actionPerformed(ActionEvent evt)
2080   {
2081
2082     SequenceGroup sg = viewport.getSelectionGroup();
2083     if (sg == null)
2084     {
2085       return;
2086     }
2087
2088     Vector seqs = new Vector();
2089     SequenceI seq;
2090     for (int i = 0; i < sg.getSize(); i++)
2091     {
2092       seq = sg.getSequenceAt(i);
2093       seqs.addElement(seq);
2094     }
2095
2096     // If the cut affects all sequences, remove highlighted columns
2097     if (sg.getSize() == viewport.getAlignment().getHeight())
2098     {
2099       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2100               sg.getEndRes() + 1);
2101     }
2102
2103     SequenceI[] cut = new SequenceI[seqs.size()];
2104     for (int i = 0; i < seqs.size(); i++)
2105     {
2106       cut[i] = (SequenceI) seqs.elementAt(i);
2107     }
2108
2109     /*
2110      * //ADD HISTORY ITEM
2111      */
2112     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2113             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2114             viewport.getAlignment()));
2115
2116     viewport.setSelectionGroup(null);
2117     viewport.sendSelection();
2118     viewport.getAlignment().deleteGroup(sg);
2119
2120     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2121             .getSequences());
2122     if (viewport.getAlignment().getHeight() < 1)
2123     {
2124       try
2125       {
2126         this.setClosed(true);
2127       } catch (Exception ex)
2128       {
2129       }
2130     }
2131   }
2132
2133   /**
2134    * DOCUMENT ME!
2135    *
2136    * @param e
2137    *          DOCUMENT ME!
2138    */
2139   @Override
2140   protected void deleteGroups_actionPerformed(ActionEvent e)
2141   {
2142     if (avc.deleteGroups()) {
2143       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2144       alignPanel.updateAnnotation();
2145       alignPanel.paintAlignment(true);
2146     }
2147   }
2148
2149   /**
2150    * DOCUMENT ME!
2151    *
2152    * @param e
2153    *          DOCUMENT ME!
2154    */
2155   @Override
2156   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2157   {
2158     SequenceGroup sg = new SequenceGroup();
2159
2160     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2161     {
2162       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2163     }
2164
2165     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2166     viewport.setSelectionGroup(sg);
2167     viewport.sendSelection();
2168     alignPanel.paintAlignment(true);
2169     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2170   }
2171
2172   /**
2173    * DOCUMENT ME!
2174    *
2175    * @param e
2176    *          DOCUMENT ME!
2177    */
2178   @Override
2179   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2180   {
2181     if (viewport.cursorMode)
2182     {
2183       alignPanel.seqPanel.keyboardNo1 = null;
2184       alignPanel.seqPanel.keyboardNo2 = null;
2185     }
2186     viewport.setSelectionGroup(null);
2187     viewport.getColumnSelection().clear();
2188     viewport.setSelectionGroup(null);
2189     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2190     alignPanel.idPanel.idCanvas.searchResults = null;
2191     alignPanel.paintAlignment(true);
2192     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2193     viewport.sendSelection();
2194   }
2195
2196   /**
2197    * DOCUMENT ME!
2198    *
2199    * @param e
2200    *          DOCUMENT ME!
2201    */
2202   @Override
2203   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2204   {
2205     SequenceGroup sg = viewport.getSelectionGroup();
2206
2207     if (sg == null)
2208     {
2209       selectAllSequenceMenuItem_actionPerformed(null);
2210
2211       return;
2212     }
2213
2214     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2215     {
2216       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2217     }
2218
2219     alignPanel.paintAlignment(true);
2220     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2221     viewport.sendSelection();
2222   }
2223
2224   @Override
2225   public void invertColSel_actionPerformed(ActionEvent e)
2226   {
2227     viewport.invertColumnSelection();
2228     alignPanel.paintAlignment(true);
2229     viewport.sendSelection();
2230   }
2231
2232   /**
2233    * DOCUMENT ME!
2234    *
2235    * @param e
2236    *          DOCUMENT ME!
2237    */
2238   @Override
2239   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2240   {
2241     trimAlignment(true);
2242   }
2243
2244   /**
2245    * DOCUMENT ME!
2246    *
2247    * @param e
2248    *          DOCUMENT ME!
2249    */
2250   @Override
2251   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2252   {
2253     trimAlignment(false);
2254   }
2255
2256   void trimAlignment(boolean trimLeft)
2257   {
2258     ColumnSelection colSel = viewport.getColumnSelection();
2259     int column;
2260
2261     if (colSel.size() > 0)
2262     {
2263       if (trimLeft)
2264       {
2265         column = colSel.getMin();
2266       }
2267       else
2268       {
2269         column = colSel.getMax();
2270       }
2271
2272       SequenceI[] seqs;
2273       if (viewport.getSelectionGroup() != null)
2274       {
2275         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2276                 viewport.getHiddenRepSequences());
2277       }
2278       else
2279       {
2280         seqs = viewport.getAlignment().getSequencesArray();
2281       }
2282
2283       TrimRegionCommand trimRegion;
2284       if (trimLeft)
2285       {
2286         trimRegion = new TrimRegionCommand("Remove Left",
2287                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2288                 viewport.getAlignment(), viewport.getColumnSelection(),
2289                 viewport.getSelectionGroup());
2290         viewport.setStartRes(0);
2291       }
2292       else
2293       {
2294         trimRegion = new TrimRegionCommand("Remove Right",
2295                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2296                 viewport.getAlignment(), viewport.getColumnSelection(),
2297                 viewport.getSelectionGroup());
2298       }
2299
2300       statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2301
2302       addHistoryItem(trimRegion);
2303
2304       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2305       {
2306         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2307                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2308         {
2309           viewport.getAlignment().deleteGroup(sg);
2310         }
2311       }
2312
2313       viewport.firePropertyChange("alignment", null, viewport
2314               .getAlignment().getSequences());
2315     }
2316   }
2317
2318   /**
2319    * DOCUMENT ME!
2320    *
2321    * @param e
2322    *          DOCUMENT ME!
2323    */
2324   @Override
2325   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2326   {
2327     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2328
2329     SequenceI[] seqs;
2330     if (viewport.getSelectionGroup() != null)
2331     {
2332       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2333               viewport.getHiddenRepSequences());
2334       start = viewport.getSelectionGroup().getStartRes();
2335       end = viewport.getSelectionGroup().getEndRes();
2336     }
2337     else
2338     {
2339       seqs = viewport.getAlignment().getSequencesArray();
2340     }
2341
2342     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2343             "Remove Gapped Columns", seqs, start, end,
2344             viewport.getAlignment());
2345
2346     addHistoryItem(removeGapCols);
2347
2348     statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2349
2350     // This is to maintain viewport position on first residue
2351     // of first sequence
2352     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2353     int startRes = seq.findPosition(viewport.startRes);
2354     // ShiftList shifts;
2355     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2356     // edit.alColumnChanges=shifts.getInverse();
2357     // if (viewport.hasHiddenColumns)
2358     // viewport.getColumnSelection().compensateForEdits(shifts);
2359     viewport.setStartRes(seq.findIndex(startRes) - 1);
2360     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2361             .getSequences());
2362
2363   }
2364
2365   /**
2366    * DOCUMENT ME!
2367    *
2368    * @param e
2369    *          DOCUMENT ME!
2370    */
2371   @Override
2372   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2373   {
2374     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2375
2376     SequenceI[] seqs;
2377     if (viewport.getSelectionGroup() != null)
2378     {
2379       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2380               viewport.getHiddenRepSequences());
2381       start = viewport.getSelectionGroup().getStartRes();
2382       end = viewport.getSelectionGroup().getEndRes();
2383     }
2384     else
2385     {
2386       seqs = viewport.getAlignment().getSequencesArray();
2387     }
2388
2389     // This is to maintain viewport position on first residue
2390     // of first sequence
2391     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2392     int startRes = seq.findPosition(viewport.startRes);
2393
2394     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2395             viewport.getAlignment()));
2396
2397     viewport.setStartRes(seq.findIndex(startRes) - 1);
2398
2399     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2400             .getSequences());
2401
2402   }
2403
2404   /**
2405    * DOCUMENT ME!
2406    *
2407    * @param e
2408    *          DOCUMENT ME!
2409    */
2410   @Override
2411   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2412   {
2413     viewport.setPadGaps(padGapsMenuitem.isSelected());
2414     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415             .getSequences());
2416   }
2417
2418   // else
2419   {
2420     // if (justifySeqs>0)
2421     {
2422       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2423     }
2424   }
2425
2426   // }
2427
2428   /**
2429    * DOCUMENT ME!
2430    *
2431    * @param e
2432    *          DOCUMENT ME!
2433    */
2434   @Override
2435   public void findMenuItem_actionPerformed(ActionEvent e)
2436   {
2437     new Finder();
2438   }
2439
2440   @Override
2441   public void newView_actionPerformed(ActionEvent e)
2442   {
2443     newView(true);
2444   }
2445
2446   /**
2447    *
2448    * @param copyAnnotation
2449    *          if true then duplicate all annnotation, groups and settings
2450    * @return new alignment panel, already displayed.
2451    */
2452   public AlignmentPanel newView(boolean copyAnnotation)
2453   {
2454     return newView(null, copyAnnotation);
2455   }
2456
2457   /**
2458    *
2459    * @param viewTitle
2460    *          title of newly created view
2461    * @return new alignment panel, already displayed.
2462    */
2463   public AlignmentPanel newView(String viewTitle)
2464   {
2465     return newView(viewTitle, true);
2466   }
2467
2468   /**
2469    *
2470    * @param viewTitle
2471    *          title of newly created view
2472    * @param copyAnnotation
2473    *          if true then duplicate all annnotation, groups and settings
2474    * @return new alignment panel, already displayed.
2475    */
2476   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2477   {
2478     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2479             true);
2480     if (!copyAnnotation)
2481     {
2482       // just remove all the current annotation except for the automatic stuff
2483       newap.av.getAlignment().deleteAllGroups();
2484       for (AlignmentAnnotation alan : newap.av.getAlignment()
2485               .getAlignmentAnnotation())
2486       {
2487         if (!alan.autoCalculated)
2488         {
2489           newap.av.getAlignment().deleteAnnotation(alan);
2490         }
2491         ;
2492       }
2493     }
2494
2495     newap.av.gatherViewsHere = false;
2496
2497     if (viewport.viewName == null)
2498     {
2499       viewport.viewName = "Original";
2500     }
2501
2502     newap.av.historyList = viewport.historyList;
2503     newap.av.redoList = viewport.redoList;
2504
2505     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2506     // make sure the new view has a unique name - this is essential for Jalview
2507     // 2 archives
2508     boolean addFirstIndex = false;
2509     if (viewTitle == null || viewTitle.trim().length() == 0)
2510     {
2511       viewTitle = "View";
2512       addFirstIndex = true;
2513     }
2514     else
2515     {
2516       index = 1;// we count from 1 if given a specific name
2517     }
2518     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2519     Vector comps = (Vector) PaintRefresher.components.get(viewport
2520             .getSequenceSetId());
2521     Vector existingNames = new Vector();
2522     for (int i = 0; i < comps.size(); i++)
2523     {
2524       if (comps.elementAt(i) instanceof AlignmentPanel)
2525       {
2526         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2527         if (!existingNames.contains(ap.av.viewName))
2528         {
2529           existingNames.addElement(ap.av.viewName);
2530         }
2531       }
2532     }
2533
2534     while (existingNames.contains(newViewName))
2535     {
2536       newViewName = viewTitle + " " + (++index);
2537     }
2538
2539     newap.av.viewName = newViewName;
2540
2541     addAlignmentPanel(newap, true);
2542     newap.alignmentChanged();
2543
2544     if (alignPanels.size() == 2)
2545     {
2546       viewport.gatherViewsHere = true;
2547     }
2548     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2549     return newap;
2550   }
2551
2552   @Override
2553   public void expandViews_actionPerformed(ActionEvent e)
2554   {
2555     Desktop.instance.explodeViews(this);
2556   }
2557
2558   @Override
2559   public void gatherViews_actionPerformed(ActionEvent e)
2560   {
2561     Desktop.instance.gatherViews(this);
2562   }
2563
2564   /**
2565    * DOCUMENT ME!
2566    *
2567    * @param e
2568    *          DOCUMENT ME!
2569    */
2570   @Override
2571   public void font_actionPerformed(ActionEvent e)
2572   {
2573     new FontChooser(alignPanel);
2574   }
2575
2576   /**
2577    * DOCUMENT ME!
2578    *
2579    * @param e
2580    *          DOCUMENT ME!
2581    */
2582   @Override
2583   protected void seqLimit_actionPerformed(ActionEvent e)
2584   {
2585     viewport.setShowJVSuffix(seqLimits.isSelected());
2586
2587     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2588             .calculateIdWidth());
2589     alignPanel.paintAlignment(true);
2590   }
2591
2592   @Override
2593   public void idRightAlign_actionPerformed(ActionEvent e)
2594   {
2595     viewport.rightAlignIds = idRightAlign.isSelected();
2596     alignPanel.paintAlignment(true);
2597   }
2598
2599   @Override
2600   public void centreColumnLabels_actionPerformed(ActionEvent e)
2601   {
2602     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2603     alignPanel.paintAlignment(true);
2604   }
2605
2606   /*
2607    * (non-Javadoc)
2608    *
2609    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2610    */
2611   @Override
2612   protected void followHighlight_actionPerformed()
2613   {
2614     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2615     {
2616       alignPanel.scrollToPosition(
2617               alignPanel.seqPanel.seqCanvas.searchResults, false);
2618     }
2619   }
2620
2621   /**
2622    * DOCUMENT ME!
2623    *
2624    * @param e
2625    *          DOCUMENT ME!
2626    */
2627   @Override
2628   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2629   {
2630     viewport.setColourText(colourTextMenuItem.isSelected());
2631     alignPanel.paintAlignment(true);
2632   }
2633
2634   /**
2635    * DOCUMENT ME!
2636    *
2637    * @param e
2638    *          DOCUMENT ME!
2639    */
2640   @Override
2641   public void wrapMenuItem_actionPerformed(ActionEvent e)
2642   {
2643     scaleAbove.setVisible(wrapMenuItem.isSelected());
2644     scaleLeft.setVisible(wrapMenuItem.isSelected());
2645     scaleRight.setVisible(wrapMenuItem.isSelected());
2646     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2647     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2648   }
2649
2650   @Override
2651   public void showAllSeqs_actionPerformed(ActionEvent e)
2652   {
2653     viewport.showAllHiddenSeqs();
2654   }
2655
2656   @Override
2657   public void showAllColumns_actionPerformed(ActionEvent e)
2658   {
2659     viewport.showAllHiddenColumns();
2660     repaint();
2661   }
2662
2663   @Override
2664   public void hideSelSequences_actionPerformed(ActionEvent e)
2665   {
2666     viewport.hideAllSelectedSeqs();
2667     alignPanel.paintAlignment(true);
2668   }
2669
2670   /**
2671    * called by key handler and the hide all/show all menu items
2672    *
2673    * @param toggleSeqs
2674    * @param toggleCols
2675    */
2676   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2677   {
2678
2679     boolean hide = false;
2680     SequenceGroup sg = viewport.getSelectionGroup();
2681     if (!toggleSeqs && !toggleCols)
2682     {
2683       // Hide everything by the current selection - this is a hack - we do the
2684       // invert and then hide
2685       // first check that there will be visible columns after the invert.
2686       if ((viewport.getColumnSelection() != null
2687               && viewport.getColumnSelection().getSelected() != null && viewport
2688               .getColumnSelection().getSelected().size() > 0)
2689               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2690                       .getEndRes()))
2691       {
2692         // now invert the sequence set, if required - empty selection implies
2693         // that no hiding is required.
2694         if (sg != null)
2695         {
2696           invertSequenceMenuItem_actionPerformed(null);
2697           sg = viewport.getSelectionGroup();
2698           toggleSeqs = true;
2699
2700         }
2701         viewport.expandColSelection(sg, true);
2702         // finally invert the column selection and get the new sequence
2703         // selection.
2704         invertColSel_actionPerformed(null);
2705         toggleCols = true;
2706       }
2707     }
2708
2709     if (toggleSeqs)
2710     {
2711       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2712       {
2713         hideSelSequences_actionPerformed(null);
2714         hide = true;
2715       }
2716       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2717               .size() > 0))
2718       {
2719         showAllSeqs_actionPerformed(null);
2720       }
2721     }
2722
2723     if (toggleCols)
2724     {
2725       if (viewport.getColumnSelection().getSelected().size() > 0)
2726       {
2727         hideSelColumns_actionPerformed(null);
2728         if (!toggleSeqs)
2729         {
2730           viewport.setSelectionGroup(sg);
2731         }
2732       }
2733       else if (!hide)
2734       {
2735         showAllColumns_actionPerformed(null);
2736       }
2737     }
2738   }
2739
2740   /*
2741    * (non-Javadoc)
2742    *
2743    * @see
2744    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2745    * event.ActionEvent)
2746    */
2747   @Override
2748   public void hideAllButSelection_actionPerformed(ActionEvent e)
2749   {
2750     toggleHiddenRegions(false, false);
2751   }
2752
2753   /*
2754    * (non-Javadoc)
2755    *
2756    * @see
2757    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2758    * .ActionEvent)
2759    */
2760   @Override
2761   public void hideAllSelection_actionPerformed(ActionEvent e)
2762   {
2763     SequenceGroup sg = viewport.getSelectionGroup();
2764     viewport.expandColSelection(sg, false);
2765     viewport.hideAllSelectedSeqs();
2766     viewport.hideSelectedColumns();
2767     alignPanel.paintAlignment(true);
2768   }
2769
2770   /*
2771    * (non-Javadoc)
2772    *
2773    * @see
2774    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2775    * ActionEvent)
2776    */
2777   @Override
2778   public void showAllhidden_actionPerformed(ActionEvent e)
2779   {
2780     viewport.showAllHiddenColumns();
2781     viewport.showAllHiddenSeqs();
2782     alignPanel.paintAlignment(true);
2783   }
2784
2785   @Override
2786   public void hideSelColumns_actionPerformed(ActionEvent e)
2787   {
2788     viewport.hideSelectedColumns();
2789     alignPanel.paintAlignment(true);
2790   }
2791
2792   @Override
2793   public void hiddenMarkers_actionPerformed(ActionEvent e)
2794   {
2795     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2796     repaint();
2797   }
2798
2799   /**
2800    * DOCUMENT ME!
2801    *
2802    * @param e
2803    *          DOCUMENT ME!
2804    */
2805   @Override
2806   protected void scaleAbove_actionPerformed(ActionEvent e)
2807   {
2808     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2809     alignPanel.paintAlignment(true);
2810   }
2811
2812   /**
2813    * DOCUMENT ME!
2814    *
2815    * @param e
2816    *          DOCUMENT ME!
2817    */
2818   @Override
2819   protected void scaleLeft_actionPerformed(ActionEvent e)
2820   {
2821     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2822     alignPanel.paintAlignment(true);
2823   }
2824
2825   /**
2826    * DOCUMENT ME!
2827    *
2828    * @param e
2829    *          DOCUMENT ME!
2830    */
2831   @Override
2832   protected void scaleRight_actionPerformed(ActionEvent e)
2833   {
2834     viewport.setScaleRightWrapped(scaleRight.isSelected());
2835     alignPanel.paintAlignment(true);
2836   }
2837
2838   /**
2839    * DOCUMENT ME!
2840    *
2841    * @param e
2842    *          DOCUMENT ME!
2843    */
2844   @Override
2845   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2846   {
2847     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2848     alignPanel.paintAlignment(true);
2849   }
2850
2851   /**
2852    * DOCUMENT ME!
2853    *
2854    * @param e
2855    *          DOCUMENT ME!
2856    */
2857   @Override
2858   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2859   {
2860     viewport.setShowText(viewTextMenuItem.isSelected());
2861     alignPanel.paintAlignment(true);
2862   }
2863
2864   /**
2865    * DOCUMENT ME!
2866    *
2867    * @param e
2868    *          DOCUMENT ME!
2869    */
2870   @Override
2871   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2874     alignPanel.paintAlignment(true);
2875   }
2876
2877   public FeatureSettings featureSettings;
2878
2879   @Override
2880   public void featureSettings_actionPerformed(ActionEvent e)
2881   {
2882     if (featureSettings != null)
2883     {
2884       featureSettings.close();
2885       featureSettings = null;
2886     }
2887     if (!showSeqFeatures.isSelected())
2888     {
2889       // make sure features are actually displayed
2890       showSeqFeatures.setSelected(true);
2891       showSeqFeatures_actionPerformed(null);
2892     }
2893     featureSettings = new FeatureSettings(this);
2894   }
2895
2896   /**
2897    * Set or clear 'Show Sequence Features'
2898    *
2899    * @param evt
2900    *          DOCUMENT ME!
2901    */
2902   @Override
2903   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2904   {
2905     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2906     alignPanel.paintAlignment(true);
2907     if (alignPanel.getOverviewPanel() != null)
2908     {
2909       alignPanel.getOverviewPanel().updateOverviewImage();
2910     }
2911   }
2912
2913   /**
2914    * Set or clear 'Show Sequence Features'
2915    *
2916    * @param evt
2917    *          DOCUMENT ME!
2918    */
2919   @Override
2920   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2921   {
2922     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2923             .isSelected());
2924     if (viewport.getShowSequenceFeaturesHeight())
2925     {
2926       // ensure we're actually displaying features
2927       viewport.setShowSequenceFeatures(true);
2928       showSeqFeatures.setSelected(true);
2929     }
2930     alignPanel.paintAlignment(true);
2931     if (alignPanel.getOverviewPanel() != null)
2932     {
2933       alignPanel.getOverviewPanel().updateOverviewImage();
2934     }
2935   }
2936
2937   /**
2938    * DOCUMENT ME!
2939    *
2940    * @param e
2941    *          DOCUMENT ME!
2942    */
2943   @Override
2944   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2945   {
2946     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2947     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2948   }
2949
2950   @Override
2951   public void alignmentProperties()
2952   {
2953     JEditorPane editPane = new JEditorPane("text/html", "");
2954     editPane.setEditable(false);
2955     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2956             .formatAsHtml();
2957     editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
2958     JInternalFrame frame = new JInternalFrame();
2959     frame.getContentPane().add(new JScrollPane(editPane));
2960
2961     Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
2962   }
2963
2964   /**
2965    * DOCUMENT ME!
2966    *
2967    * @param e
2968    *          DOCUMENT ME!
2969    */
2970   @Override
2971   public void overviewMenuItem_actionPerformed(ActionEvent e)
2972   {
2973     if (alignPanel.overviewPanel != null)
2974     {
2975       return;
2976     }
2977
2978     JInternalFrame frame = new JInternalFrame();
2979     OverviewPanel overview = new OverviewPanel(alignPanel);
2980     frame.setContentPane(overview);
2981     Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
2982             frame.getWidth(), frame.getHeight());
2983     frame.pack();
2984     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2985     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2986     {
2987       @Override
2988       public void internalFrameClosed(
2989               javax.swing.event.InternalFrameEvent evt)
2990       {
2991         alignPanel.setOverviewPanel(null);
2992       };
2993     });
2994
2995     alignPanel.setOverviewPanel(overview);
2996   }
2997
2998   @Override
2999   public void textColour_actionPerformed(ActionEvent e)
3000   {
3001     new TextColourChooser().chooseColour(alignPanel, null);
3002   }
3003
3004   /**
3005    * DOCUMENT ME!
3006    *
3007    * @param e
3008    *          DOCUMENT ME!
3009    */
3010   @Override
3011   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3012   {
3013     changeColour(null);
3014   }
3015
3016   /**
3017    * DOCUMENT ME!
3018    *
3019    * @param e
3020    *          DOCUMENT ME!
3021    */
3022   @Override
3023   public void clustalColour_actionPerformed(ActionEvent e)
3024   {
3025     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3026             viewport.getHiddenRepSequences()));
3027   }
3028
3029   /**
3030    * DOCUMENT ME!
3031    *
3032    * @param e
3033    *          DOCUMENT ME!
3034    */
3035   @Override
3036   public void zappoColour_actionPerformed(ActionEvent e)
3037   {
3038     changeColour(new ZappoColourScheme());
3039   }
3040
3041   /**
3042    * DOCUMENT ME!
3043    *
3044    * @param e
3045    *          DOCUMENT ME!
3046    */
3047   @Override
3048   public void taylorColour_actionPerformed(ActionEvent e)
3049   {
3050     changeColour(new TaylorColourScheme());
3051   }
3052
3053   /**
3054    * DOCUMENT ME!
3055    *
3056    * @param e
3057    *          DOCUMENT ME!
3058    */
3059   @Override
3060   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3061   {
3062     changeColour(new HydrophobicColourScheme());
3063   }
3064
3065   /**
3066    * DOCUMENT ME!
3067    *
3068    * @param e
3069    *          DOCUMENT ME!
3070    */
3071   @Override
3072   public void helixColour_actionPerformed(ActionEvent e)
3073   {
3074     changeColour(new HelixColourScheme());
3075   }
3076
3077   /**
3078    * DOCUMENT ME!
3079    *
3080    * @param e
3081    *          DOCUMENT ME!
3082    */
3083   @Override
3084   public void strandColour_actionPerformed(ActionEvent e)
3085   {
3086     changeColour(new StrandColourScheme());
3087   }
3088
3089   /**
3090    * DOCUMENT ME!
3091    *
3092    * @param e
3093    *          DOCUMENT ME!
3094    */
3095   @Override
3096   public void turnColour_actionPerformed(ActionEvent e)
3097   {
3098     changeColour(new TurnColourScheme());
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   public void buriedColour_actionPerformed(ActionEvent e)
3109   {
3110     changeColour(new BuriedColourScheme());
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   public void nucleotideColour_actionPerformed(ActionEvent e)
3121   {
3122     changeColour(new NucleotideColourScheme());
3123   }
3124
3125   @Override
3126   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3127   {
3128     changeColour(new PurinePyrimidineColourScheme());
3129   }
3130
3131   /*
3132    * public void covariationColour_actionPerformed(ActionEvent e) {
3133    * changeColour(new
3134    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3135    * ()[0])); }
3136    */
3137   @Override
3138   public void annotationColour_actionPerformed(ActionEvent e)
3139   {
3140     new AnnotationColourChooser(viewport, alignPanel);
3141   }
3142
3143   @Override
3144   public void rnahelicesColour_actionPerformed(ActionEvent e)
3145   {
3146     new RNAHelicesColourChooser(viewport, alignPanel);
3147   }
3148
3149   /**
3150    * DOCUMENT ME!
3151    *
3152    * @param e
3153    *          DOCUMENT ME!
3154    */
3155   @Override
3156   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3157   {
3158     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param cs
3165    *          DOCUMENT ME!
3166    */
3167   public void changeColour(ColourSchemeI cs)
3168   {
3169     // TODO: compare with applet and pull up to model method
3170     int threshold = 0;
3171
3172     if (cs != null)
3173     {
3174       if (viewport.getAbovePIDThreshold())
3175       {
3176         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3177                 "Background");
3178
3179         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3180
3181         viewport.setGlobalColourScheme(cs);
3182       }
3183       else
3184       {
3185         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3186       }
3187
3188       if (viewport.getConservationSelected())
3189       {
3190
3191         Alignment al = (Alignment) viewport.getAlignment();
3192         Conservation c = new Conservation("All",
3193                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3194                 al.getWidth() - 1);
3195
3196         c.calculate();
3197         c.verdict(false, viewport.getConsPercGaps());
3198
3199         cs.setConservation(c);
3200
3201         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3202                 cs, "Background"));
3203       }
3204       else
3205       {
3206         cs.setConservation(null);
3207       }
3208
3209       cs.setConsensus(viewport.getSequenceConsensusHash());
3210     }
3211
3212     viewport.setGlobalColourScheme(cs);
3213
3214     if (viewport.getColourAppliesToAllGroups())
3215     {
3216
3217       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3218       {
3219         if (cs == null)
3220         {
3221           sg.cs = null;
3222           continue;
3223         }
3224
3225         if (cs instanceof ClustalxColourScheme)
3226         {
3227           sg.cs = new ClustalxColourScheme(sg,
3228                   viewport.getHiddenRepSequences());
3229         }
3230         else if (cs instanceof UserColourScheme)
3231         {
3232           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3233         }
3234         else
3235         {
3236           try
3237           {
3238             sg.cs = cs.getClass().newInstance();
3239           } catch (Exception ex)
3240           {
3241           }
3242         }
3243
3244         if (viewport.getAbovePIDThreshold()
3245                 || cs instanceof PIDColourScheme
3246                 || cs instanceof Blosum62ColourScheme)
3247         {
3248           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3249
3250           sg.cs.setConsensus(AAFrequency.calculate(
3251                   sg.getSequences(viewport.getHiddenRepSequences()),
3252                   sg.getStartRes(), sg.getEndRes() + 1));
3253         }
3254         else
3255         {
3256           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3257         }
3258
3259         if (viewport.getConservationSelected())
3260         {
3261           Conservation c = new Conservation("Group",
3262                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3263                           .getHiddenRepSequences()), sg.getStartRes(),
3264                   sg.getEndRes() + 1);
3265           c.calculate();
3266           c.verdict(false, viewport.getConsPercGaps());
3267           sg.cs.setConservation(c);
3268         }
3269         else
3270         {
3271           sg.cs.setConservation(null);
3272         }
3273       }
3274     }
3275
3276     if (alignPanel.getOverviewPanel() != null)
3277     {
3278       alignPanel.getOverviewPanel().updateOverviewImage();
3279     }
3280
3281     alignPanel.paintAlignment(true);
3282   }
3283
3284   /**
3285    * DOCUMENT ME!
3286    *
3287    * @param e
3288    *          DOCUMENT ME!
3289    */
3290   @Override
3291   protected void modifyPID_actionPerformed(ActionEvent e)
3292   {
3293     if (viewport.getAbovePIDThreshold()
3294             && viewport.getGlobalColourScheme() != null)
3295     {
3296       SliderPanel.setPIDSliderSource(alignPanel,
3297               viewport.getGlobalColourScheme(), "Background");
3298       SliderPanel.showPIDSlider();
3299     }
3300   }
3301
3302   /**
3303    * DOCUMENT ME!
3304    *
3305    * @param e
3306    *          DOCUMENT ME!
3307    */
3308   @Override
3309   protected void modifyConservation_actionPerformed(ActionEvent e)
3310   {
3311     if (viewport.getConservationSelected()
3312             && viewport.getGlobalColourScheme() != null)
3313     {
3314       SliderPanel.setConservationSlider(alignPanel,
3315               viewport.getGlobalColourScheme(), "Background");
3316       SliderPanel.showConservationSlider();
3317     }
3318   }
3319
3320   /**
3321    * DOCUMENT ME!
3322    *
3323    * @param e
3324    *          DOCUMENT ME!
3325    */
3326   @Override
3327   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3328   {
3329     viewport.setConservationSelected(conservationMenuItem.isSelected());
3330
3331     viewport.setAbovePIDThreshold(false);
3332     abovePIDThreshold.setSelected(false);
3333
3334     changeColour(viewport.getGlobalColourScheme());
3335
3336     modifyConservation_actionPerformed(null);
3337   }
3338
3339   /**
3340    * DOCUMENT ME!
3341    *
3342    * @param e
3343    *          DOCUMENT ME!
3344    */
3345   @Override
3346   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3347   {
3348     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3349
3350     conservationMenuItem.setSelected(false);
3351     viewport.setConservationSelected(false);
3352
3353     changeColour(viewport.getGlobalColourScheme());
3354
3355     modifyPID_actionPerformed(null);
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   public void userDefinedColour_actionPerformed(ActionEvent e)
3366   {
3367     if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
3368     {
3369       new UserDefinedColours(alignPanel, null);
3370     }
3371     else
3372     {
3373       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3374               .getUserColourSchemes().get(e.getActionCommand());
3375
3376       changeColour(udc);
3377     }
3378   }
3379
3380   public void updateUserColourMenu()
3381   {
3382
3383     Component[] menuItems = colourMenu.getMenuComponents();
3384     int i, iSize = menuItems.length;
3385     for (i = 0; i < iSize; i++)
3386     {
3387       if (menuItems[i].getName() != null
3388               && menuItems[i].getName().equals("USER_DEFINED"))
3389       {
3390         colourMenu.remove(menuItems[i]);
3391         iSize--;
3392       }
3393     }
3394     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3395     {
3396       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3397               .getUserColourSchemes().keys();
3398
3399       while (userColours.hasMoreElements())
3400       {
3401         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3402                 userColours.nextElement().toString());
3403         radioItem.setName("USER_DEFINED");
3404         radioItem.addMouseListener(new MouseAdapter()
3405         {
3406           @Override
3407           public void mousePressed(MouseEvent evt)
3408           {
3409             if (evt.isControlDown()
3410                     || SwingUtilities.isRightMouseButton(evt))
3411             {
3412               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3413
3414               int option = JOptionPane.showInternalConfirmDialog(
3415                       jalview.gui.Desktop.desktop,
3416                       MessageManager.getString("label.remove_from_default_list"),
3417                       MessageManager.getString("label.remove_user_defined_colour"),
3418                       JOptionPane.YES_NO_OPTION);
3419               if (option == JOptionPane.YES_OPTION)
3420               {
3421                 jalview.gui.UserDefinedColours
3422                         .removeColourFromDefaults(radioItem.getText());
3423                 colourMenu.remove(radioItem);
3424               }
3425               else
3426               {
3427                 radioItem.addActionListener(new ActionListener()
3428                 {
3429                   @Override
3430                   public void actionPerformed(ActionEvent evt)
3431                   {
3432                     userDefinedColour_actionPerformed(evt);
3433                   }
3434                 });
3435               }
3436             }
3437           }
3438         });
3439         radioItem.addActionListener(new ActionListener()
3440         {
3441           @Override
3442           public void actionPerformed(ActionEvent evt)
3443           {
3444             userDefinedColour_actionPerformed(evt);
3445           }
3446         });
3447
3448         colourMenu.insert(radioItem, 15);
3449         colours.add(radioItem);
3450       }
3451     }
3452   }
3453
3454   /**
3455    * DOCUMENT ME!
3456    *
3457    * @param e
3458    *          DOCUMENT ME!
3459    */
3460   @Override
3461   public void PIDColour_actionPerformed(ActionEvent e)
3462   {
3463     changeColour(new PIDColourScheme());
3464   }
3465
3466   /**
3467    * DOCUMENT ME!
3468    *
3469    * @param e
3470    *          DOCUMENT ME!
3471    */
3472   @Override
3473   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3474   {
3475     changeColour(new Blosum62ColourScheme());
3476   }
3477
3478   /**
3479    * DOCUMENT ME!
3480    *
3481    * @param e
3482    *          DOCUMENT ME!
3483    */
3484   @Override
3485   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3486   {
3487     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3489             .getAlignment().getSequenceAt(0), null);
3490     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3491             viewport.getAlignment()));
3492     alignPanel.paintAlignment(true);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505     AlignmentSorter.sortByID(viewport.getAlignment());
3506     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3507             viewport.getAlignment()));
3508     alignPanel.paintAlignment(true);
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521     AlignmentSorter.sortByLength(viewport.getAlignment());
3522     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3523             viewport.getAlignment()));
3524     alignPanel.paintAlignment(true);
3525   }
3526
3527   /**
3528    * DOCUMENT ME!
3529    *
3530    * @param e
3531    *          DOCUMENT ME!
3532    */
3533   @Override
3534   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3535   {
3536     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3537     AlignmentSorter.sortByGroup(viewport.getAlignment());
3538     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3539             viewport.getAlignment()));
3540
3541     alignPanel.paintAlignment(true);
3542   }
3543
3544   /**
3545    * DOCUMENT ME!
3546    *
3547    * @param e
3548    *          DOCUMENT ME!
3549    */
3550   @Override
3551   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3552   {
3553     new RedundancyPanel(alignPanel, this);
3554   }
3555
3556   /**
3557    * DOCUMENT ME!
3558    *
3559    * @param e
3560    *          DOCUMENT ME!
3561    */
3562   @Override
3563   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3564   {
3565     if ((viewport.getSelectionGroup() == null)
3566             || (viewport.getSelectionGroup().getSize() < 2))
3567     {
3568       JOptionPane.showInternalMessageDialog(this,
3569               MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
3570               JOptionPane.WARNING_MESSAGE);
3571     }
3572     else
3573     {
3574       JInternalFrame frame = new JInternalFrame();
3575       frame.setContentPane(new PairwiseAlignPanel(viewport));
3576       Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
3577     }
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void PCAMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     if (((viewport.getSelectionGroup() != null)
3590             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3591             .getSelectionGroup().getSize() > 0))
3592             || (viewport.getAlignment().getHeight() < 4))
3593     {
3594       JOptionPane.showInternalMessageDialog(this,
3595               MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3596               MessageManager.getString("label.sequence_selection_insufficient"),
3597               JOptionPane.WARNING_MESSAGE);
3598
3599       return;
3600     }
3601
3602     new PCAPanel(alignPanel);
3603   }
3604
3605   @Override
3606   public void autoCalculate_actionPerformed(ActionEvent e)
3607   {
3608     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3609     if (viewport.autoCalculateConsensus)
3610     {
3611       viewport.firePropertyChange("alignment", null, viewport
3612               .getAlignment().getSequences());
3613     }
3614   }
3615
3616   @Override
3617   public void sortByTreeOption_actionPerformed(ActionEvent e)
3618   {
3619     viewport.sortByTree = sortByTree.isSelected();
3620   }
3621
3622   @Override
3623   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3624   {
3625     viewport.followSelection = listenToViewSelections.isSelected();
3626   }
3627
3628   /**
3629    * DOCUMENT ME!
3630    *
3631    * @param e
3632    *          DOCUMENT ME!
3633    */
3634   @Override
3635   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3636   {
3637     NewTreePanel("AV", "PID", "Average distance tree using PID");
3638   }
3639
3640   /**
3641    * DOCUMENT ME!
3642    *
3643    * @param e
3644    *          DOCUMENT ME!
3645    */
3646   @Override
3647   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3648   {
3649     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3650   }
3651
3652   /**
3653    * DOCUMENT ME!
3654    *
3655    * @param e
3656    *          DOCUMENT ME!
3657    */
3658   @Override
3659   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3660   {
3661     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3662   }
3663
3664   /**
3665    * DOCUMENT ME!
3666    *
3667    * @param e
3668    *          DOCUMENT ME!
3669    */
3670   @Override
3671   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3672   {
3673     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3674   }
3675
3676   /**
3677    * DOCUMENT ME!
3678    *
3679    * @param type
3680    *          DOCUMENT ME!
3681    * @param pwType
3682    *          DOCUMENT ME!
3683    * @param title
3684    *          DOCUMENT ME!
3685    */
3686   void NewTreePanel(String type, String pwType, String title)
3687   {
3688     TreePanel tp;
3689
3690     if (viewport.getSelectionGroup() != null
3691             && viewport.getSelectionGroup().getSize() > 0)
3692     {
3693       if (viewport.getSelectionGroup().getSize() < 3)
3694       {
3695         JOptionPane
3696                 .showMessageDialog(
3697                         Desktop.desktop,
3698                         MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
3699                         MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
3700         return;
3701       }
3702
3703       SequenceGroup sg = viewport.getSelectionGroup();
3704
3705       /* Decide if the selection is a column region */
3706       for (SequenceI _s : sg.getSequences())
3707       {
3708         if (_s.getLength() < sg.getEndRes())
3709         {
3710           JOptionPane
3711                   .showMessageDialog(
3712                           Desktop.desktop,
3713                           MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3714                           MessageManager.getString("label.sequences_selection_not_aligned"),
3715                           JOptionPane.WARNING_MESSAGE);
3716
3717           return;
3718         }
3719       }
3720
3721       title = title + " on region";
3722       tp = new TreePanel(alignPanel, type, pwType);
3723     }
3724     else
3725     {
3726       // are the visible sequences aligned?
3727       if (!viewport.getAlignment().isAligned(false))
3728       {
3729         JOptionPane
3730                 .showMessageDialog(
3731                         Desktop.desktop,
3732                         MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
3733                         MessageManager.getString("label.sequences_not_aligned"),
3734                         JOptionPane.WARNING_MESSAGE);
3735
3736         return;
3737       }
3738
3739       if (viewport.getAlignment().getHeight() < 2)
3740       {
3741         return;
3742       }
3743
3744       tp = new TreePanel(alignPanel, type, pwType);
3745     }
3746
3747     title += " from ";
3748
3749     if (viewport.viewName != null)
3750     {
3751       title += viewport.viewName + " of ";
3752     }
3753
3754     title += this.title;
3755
3756     Desktop.addInternalFrame(tp, title, 600, 500);
3757   }
3758
3759   /**
3760    * DOCUMENT ME!
3761    *
3762    * @param title
3763    *          DOCUMENT ME!
3764    * @param order
3765    *          DOCUMENT ME!
3766    */
3767   public void addSortByOrderMenuItem(String title,
3768           final AlignmentOrder order)
3769   {
3770     final JMenuItem item = new JMenuItem("by " + title);
3771     sort.add(item);
3772     item.addActionListener(new java.awt.event.ActionListener()
3773     {
3774       @Override
3775       public void actionPerformed(ActionEvent e)
3776       {
3777         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778
3779         // TODO: JBPNote - have to map order entries to curent SequenceI
3780         // pointers
3781         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3782
3783         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3784                 .getAlignment()));
3785
3786         alignPanel.paintAlignment(true);
3787       }
3788     });
3789   }
3790
3791   /**
3792    * Add a new sort by annotation score menu item
3793    *
3794    * @param sort
3795    *          the menu to add the option to
3796    * @param scoreLabel
3797    *          the label used to retrieve scores for each sequence on the
3798    *          alignment
3799    */
3800   public void addSortByAnnotScoreMenuItem(JMenu sort,
3801           final String scoreLabel)
3802   {
3803     final JMenuItem item = new JMenuItem(scoreLabel);
3804     sort.add(item);
3805     item.addActionListener(new java.awt.event.ActionListener()
3806     {
3807       @Override
3808       public void actionPerformed(ActionEvent e)
3809       {
3810         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3811         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3812                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3813         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3814                 viewport.getAlignment()));
3815         alignPanel.paintAlignment(true);
3816       }
3817     });
3818   }
3819
3820   /**
3821    * last hash for alignment's annotation array - used to minimise cost of
3822    * rebuild.
3823    */
3824   protected int _annotationScoreVectorHash;
3825
3826   /**
3827    * search the alignment and rebuild the sort by annotation score submenu the
3828    * last alignment annotation vector hash is stored to minimize cost of
3829    * rebuilding in subsequence calls.
3830    *
3831    */
3832   @Override
3833   public void buildSortByAnnotationScoresMenu()
3834   {
3835     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3836     {
3837       return;
3838     }
3839
3840     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3841     {
3842       sortByAnnotScore.removeAll();
3843       // almost certainly a quicker way to do this - but we keep it simple
3844       Hashtable scoreSorts = new Hashtable();
3845       AlignmentAnnotation aann[];
3846       for (SequenceI sqa : viewport.getAlignment().getSequences())
3847       {
3848         aann = sqa.getAnnotation();
3849         for (int i = 0; aann != null && i < aann.length; i++)
3850         {
3851           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3852           {
3853             scoreSorts.put(aann[i].label, aann[i].label);
3854           }
3855         }
3856       }
3857       Enumeration labels = scoreSorts.keys();
3858       while (labels.hasMoreElements())
3859       {
3860         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3861                 (String) labels.nextElement());
3862       }
3863       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3864       scoreSorts.clear();
3865
3866       _annotationScoreVectorHash = viewport.getAlignment()
3867               .getAlignmentAnnotation().hashCode();
3868     }
3869   }
3870
3871   /**
3872    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3873    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3874    * call. Listeners are added to remove the menu item when the treePanel is
3875    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3876    * modified.
3877    *
3878    * @param treePanel
3879    *          Displayed tree window.
3880    * @param title
3881    *          SortBy menu item title.
3882    */
3883   @Override
3884   public void buildTreeMenu()
3885   {
3886     sortByTreeMenu.removeAll();
3887
3888     Vector comps = (Vector) PaintRefresher.components.get(viewport
3889             .getSequenceSetId());
3890     Vector treePanels = new Vector();
3891     int i, iSize = comps.size();
3892     for (i = 0; i < iSize; i++)
3893     {
3894       if (comps.elementAt(i) instanceof TreePanel)
3895       {
3896         treePanels.add(comps.elementAt(i));
3897       }
3898     }
3899
3900     iSize = treePanels.size();
3901
3902     if (iSize < 1)
3903     {
3904       sortByTreeMenu.setVisible(false);
3905       return;
3906     }
3907
3908     sortByTreeMenu.setVisible(true);
3909
3910     for (i = 0; i < treePanels.size(); i++)
3911     {
3912       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3913       final JMenuItem item = new JMenuItem(tp.getTitle());
3914       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3915       item.addActionListener(new java.awt.event.ActionListener()
3916       {
3917         @Override
3918         public void actionPerformed(ActionEvent e)
3919         {
3920           tp.sortByTree_actionPerformed(null);
3921           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3922
3923         }
3924       });
3925
3926       sortByTreeMenu.add(item);
3927     }
3928   }
3929
3930   public boolean sortBy(AlignmentOrder alorder, String undoname)
3931   {
3932     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3933     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3934     if (undoname != null)
3935     {
3936       addHistoryItem(new OrderCommand(undoname, oldOrder,
3937               viewport.getAlignment()));
3938     }
3939     alignPanel.paintAlignment(true);
3940     return true;
3941   }
3942
3943   /**
3944    * Work out whether the whole set of sequences or just the selected set will
3945    * be submitted for multiple alignment.
3946    *
3947    */
3948   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3949   {
3950     // Now, check we have enough sequences
3951     AlignmentView msa = null;
3952
3953     if ((viewport.getSelectionGroup() != null)
3954             && (viewport.getSelectionGroup().getSize() > 1))
3955     {
3956       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3957       // some common interface!
3958       /*
3959        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3960        * SequenceI[sz = seqs.getSize(false)];
3961        *
3962        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3963        * seqs.getSequenceAt(i); }
3964        */
3965       msa = viewport.getAlignmentView(true);
3966     }
3967     else
3968     {
3969       /*
3970        * Vector seqs = viewport.getAlignment().getSequences();
3971        *
3972        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3973        *
3974        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3975        * seqs.elementAt(i); } }
3976        */
3977       msa = viewport.getAlignmentView(false);
3978     }
3979     return msa;
3980   }
3981
3982   /**
3983    * Decides what is submitted to a secondary structure prediction service: the
3984    * first sequence in the alignment, or in the current selection, or, if the
3985    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3986    * region or the whole alignment. (where the first sequence in the set is the
3987    * one that the prediction will be for).
3988    */
3989   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3990   {
3991     AlignmentView seqs = null;
3992
3993     if ((viewport.getSelectionGroup() != null)
3994             && (viewport.getSelectionGroup().getSize() > 0))
3995     {
3996       seqs = viewport.getAlignmentView(true);
3997     }
3998     else
3999     {
4000       seqs = viewport.getAlignmentView(false);
4001     }
4002     // limit sequences - JBPNote in future - could spawn multiple prediction
4003     // jobs
4004     // TODO: viewport.getAlignment().isAligned is a global state - the local
4005     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4006     if (!viewport.getAlignment().isAligned(false))
4007     {
4008       seqs.setSequences(new SeqCigar[]
4009       { seqs.getSequences()[0] });
4010       // TODO: if seqs.getSequences().length>1 then should really have warned
4011       // user!
4012
4013     }
4014     return seqs;
4015   }
4016
4017   /**
4018    * DOCUMENT ME!
4019    *
4020    * @param e
4021    *          DOCUMENT ME!
4022    */
4023   @Override
4024   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4025   {
4026     // Pick the tree file
4027     JalviewFileChooser chooser = new JalviewFileChooser(
4028             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4029     chooser.setFileView(new JalviewFileView());
4030     chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
4031     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
4032
4033     int value = chooser.showOpenDialog(null);
4034
4035     if (value == JalviewFileChooser.APPROVE_OPTION)
4036     {
4037       String choice = chooser.getSelectedFile().getPath();
4038       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4039       jalview.io.NewickFile fin = null;
4040       try
4041       {
4042         fin = new jalview.io.NewickFile(choice, "File");
4043         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4044       } catch (Exception ex)
4045       {
4046         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4047                 MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
4048         ex.printStackTrace();
4049       }
4050       if (fin != null && fin.hasWarningMessage())
4051       {
4052         JOptionPane.showMessageDialog(Desktop.desktop,
4053                 fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
4054                 JOptionPane.WARNING_MESSAGE);
4055       }
4056     }
4057   }
4058
4059   @Override
4060   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4061   {
4062     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4063   }
4064
4065   public TreePanel ShowNewickTree(NewickFile nf, String title)
4066   {
4067     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4068   }
4069
4070   public TreePanel ShowNewickTree(NewickFile nf, String title,
4071           AlignmentView input)
4072   {
4073     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4074   }
4075
4076   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4077           int h, int x, int y)
4078   {
4079     return ShowNewickTree(nf, title, null, w, h, x, y);
4080   }
4081
4082   /**
4083    * Add a treeviewer for the tree extracted from a newick file object to the
4084    * current alignment view
4085    *
4086    * @param nf
4087    *          the tree
4088    * @param title
4089    *          tree viewer title
4090    * @param input
4091    *          Associated alignment input data (or null)
4092    * @param w
4093    *          width
4094    * @param h
4095    *          height
4096    * @param x
4097    *          position
4098    * @param y
4099    *          position
4100    * @return TreePanel handle
4101    */
4102   public TreePanel ShowNewickTree(NewickFile nf, String title,
4103           AlignmentView input, int w, int h, int x, int y)
4104   {
4105     TreePanel tp = null;
4106
4107     try
4108     {
4109       nf.parse();
4110
4111       if (nf.getTree() != null)
4112       {
4113         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4114
4115         tp.setSize(w, h);
4116
4117         if (x > 0 && y > 0)
4118         {
4119           tp.setLocation(x, y);
4120         }
4121
4122         Desktop.addInternalFrame(tp, title, w, h);
4123       }
4124     } catch (Exception ex)
4125     {
4126       ex.printStackTrace();
4127     }
4128
4129     return tp;
4130   }
4131
4132   private boolean buildingMenu = false;
4133
4134   /**
4135    * Generates menu items and listener event actions for web service clients
4136    *
4137    */
4138   public void BuildWebServiceMenu()
4139   {
4140     while (buildingMenu)
4141     {
4142       try
4143       {
4144         System.err.println("Waiting for building menu to finish.");
4145         Thread.sleep(10);
4146       } catch (Exception e)
4147       {
4148       }
4149       ;
4150     }
4151     final AlignFrame me = this;
4152     buildingMenu = true;
4153     new Thread(new Runnable()
4154     {
4155       @Override
4156       public void run()
4157       {
4158         final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
4159         try
4160         {
4161           System.err.println("Building ws menu again "
4162                   + Thread.currentThread());
4163           // TODO: add support for context dependent disabling of services based
4164           // on
4165           // alignment and current selection
4166           // TODO: add additional serviceHandle parameter to specify abstract
4167           // handler
4168           // class independently of AbstractName
4169           // TODO: add in rediscovery GUI function to restart discoverer
4170           // TODO: group services by location as well as function and/or
4171           // introduce
4172           // object broker mechanism.
4173           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4174           final IProgressIndicator af = me;
4175           final JMenu msawsmenu = new JMenu("Alignment");
4176           final JMenu secstrmenu = new JMenu(
4177                   "Secondary Structure Prediction");
4178           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4179           final JMenu analymenu = new JMenu("Analysis");
4180           final JMenu dismenu = new JMenu("Protein Disorder");
4181           // JAL-940 - only show secondary structure prediction services from
4182           // the legacy server
4183           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4184               // &&
4185           Discoverer.services != null && (Discoverer.services.size() > 0))
4186           {
4187             // TODO: refactor to allow list of AbstractName/Handler bindings to
4188             // be
4189             // stored or retrieved from elsewhere
4190             // No MSAWS used any more:
4191             // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4192             Vector secstrpr = (Vector) Discoverer.services
4193                     .get("SecStrPred");
4194             if (secstrpr != null)
4195             {
4196               // Add any secondary structure prediction services
4197               for (int i = 0, j = secstrpr.size(); i < j; i++)
4198               {
4199                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4200                         .get(i);
4201                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4202                         .getServiceClient(sh);
4203                 int p=secstrmenu.getItemCount();
4204                 impl.attachWSMenuEntry(secstrmenu, me);
4205                 int q=secstrmenu.getItemCount();
4206                 for (int litm=p;litm<q; litm++)
4207                 {
4208                   legacyItems.add(secstrmenu.getItem(litm));
4209                 }
4210               }
4211             }
4212           }
4213
4214           // Add all submenus in the order they should appear on the web
4215           // services menu
4216           wsmenu.add(msawsmenu);
4217           wsmenu.add(secstrmenu);
4218           wsmenu.add(dismenu);
4219           wsmenu.add(analymenu);
4220           // No search services yet
4221           // wsmenu.add(seqsrchmenu);
4222
4223           javax.swing.SwingUtilities.invokeLater(new Runnable()
4224           {
4225             @Override
4226             public void run()
4227             {
4228               try
4229               {
4230                 webService.removeAll();
4231                 // first, add discovered services onto the webservices menu
4232                 if (wsmenu.size() > 0)
4233                 {
4234                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4235                   {
4236                     webService.add(wsmenu.get(i));
4237                   }
4238                 }
4239                 else
4240                 {
4241                   webService.add(me.webServiceNoServices);
4242                 }
4243                 // TODO: move into separate menu builder class.
4244                 boolean new_sspred=false;
4245                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4246                 {
4247                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4248                   if (jws2servs != null)
4249                   {
4250                     if (jws2servs.hasServices())
4251                     {
4252                       jws2servs.attachWSMenuEntry(webService, me);
4253                       for (Jws2Instance sv:jws2servs.getServices()) {
4254                         if (sv.description.toLowerCase().contains("jpred"))
4255                         {
4256                           for (JMenuItem jmi:legacyItems)
4257                           {
4258                             jmi.setVisible(false);
4259                           }
4260                         }
4261                       }
4262
4263                     }
4264                     if (jws2servs.isRunning())
4265                     {
4266                       JMenuItem tm = new JMenuItem(
4267                               "Still discovering JABA Services");
4268                       tm.setEnabled(false);
4269                       webService.add(tm);
4270                     }
4271                   }
4272                 }
4273                 build_urlServiceMenu(me.webService);
4274                 build_fetchdbmenu(webService);
4275                 for (JMenu item : wsmenu)
4276                 {
4277                   if (item.getItemCount() == 0)
4278                   {
4279                     item.setEnabled(false);
4280                   }
4281                   else
4282                   {
4283                     item.setEnabled(true);
4284                   }
4285                 }
4286               } catch (Exception e)
4287               {
4288                 Cache.log
4289                         .debug("Exception during web service menu building process.",
4290                                 e);
4291               }
4292               ;
4293             }
4294           });
4295         } catch (Exception e)
4296         {
4297         }
4298         ;
4299
4300         buildingMenu = false;
4301       }
4302     }).start();
4303
4304   }
4305
4306   /**
4307    * construct any groupURL type service menu entries.
4308    *
4309    * @param webService
4310    */
4311   private void build_urlServiceMenu(JMenu webService)
4312   {
4313     // TODO: remove this code when 2.7 is released
4314     // DEBUG - alignmentView
4315     /*
4316      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4317      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4318      *
4319      * @Override public void actionPerformed(ActionEvent e) {
4320      * jalview.datamodel.AlignmentView
4321      * .testSelectionViews(af.viewport.getAlignment(),
4322      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4323      *
4324      * }); webService.add(testAlView);
4325      */
4326     // TODO: refactor to RestClient discoverer and merge menu entries for
4327     // rest-style services with other types of analysis/calculation service
4328     // SHmmr test client - still being implemented.
4329     // DEBUG - alignmentView
4330
4331     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4332             .getRestClients())
4333     {
4334       client.attachWSMenuEntry(
4335               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4336               this);
4337     }
4338
4339     if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4340     {
4341       jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4342               webService, this);
4343     }
4344   }
4345
4346   /*
4347    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4348    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4349    * getProperty("LAST_DIRECTORY"));
4350    *
4351    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4352    * to Vamsas file"); chooser.setToolTipText("Export");
4353    *
4354    * int value = chooser.showSaveDialog(this);
4355    *
4356    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4357    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4358    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4359    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4360    */
4361   /**
4362    * prototype of an automatically enabled/disabled analysis function
4363    *
4364    */
4365   protected void setShowProductsEnabled()
4366   {
4367     SequenceI[] selection = viewport.getSequenceSelection();
4368     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4369             viewport.getAlignment().getDataset()))
4370     {
4371       showProducts.setEnabled(true);
4372
4373     }
4374     else
4375     {
4376       showProducts.setEnabled(false);
4377     }
4378   }
4379
4380   /**
4381    * search selection for sequence xRef products and build the show products
4382    * menu.
4383    *
4384    * @param selection
4385    * @param dataset
4386    * @return true if showProducts menu should be enabled.
4387    */
4388   public boolean canShowProducts(SequenceI[] selection,
4389           boolean isRegionSelection, Alignment dataset)
4390   {
4391     boolean showp = false;
4392     try
4393     {
4394       showProducts.removeAll();
4395       final boolean dna = viewport.getAlignment().isNucleotide();
4396       final Alignment ds = dataset;
4397       String[] ptypes = (selection == null || selection.length == 0) ? null
4398               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4399       // Object[] prods =
4400       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4401       // selection, dataset, true);
4402       final SequenceI[] sel = selection;
4403       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4404       {
4405         showp = true;
4406         final boolean isRegSel = isRegionSelection;
4407         final AlignFrame af = this;
4408         final String source = ptypes[t];
4409         JMenuItem xtype = new JMenuItem(ptypes[t]);
4410         xtype.addActionListener(new ActionListener()
4411         {
4412
4413           @Override
4414           public void actionPerformed(ActionEvent e)
4415           {
4416             // TODO: new thread for this call with vis-delay
4417             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4418                     isRegSel, dna, source);
4419           }
4420
4421         });
4422         showProducts.add(xtype);
4423       }
4424       showProducts.setVisible(showp);
4425       showProducts.setEnabled(showp);
4426     } catch (Exception e)
4427     {
4428       jalview.bin.Cache.log
4429               .warn("canTranslate threw an exception - please report to help@jalview.org",
4430                       e);
4431       return false;
4432     }
4433     return showp;
4434   }
4435
4436   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4437           boolean isRegSel, boolean dna, String source)
4438   {
4439     final boolean fisRegSel = isRegSel;
4440     final boolean fdna = dna;
4441     final String fsrc = source;
4442     final AlignFrame ths = this;
4443     final SequenceI[] fsel = sel;
4444     Runnable foo = new Runnable()
4445     {
4446
4447       @Override
4448       public void run()
4449       {
4450         final long sttime = System.currentTimeMillis();
4451         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4452         try
4453         {
4454           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4455           // our local
4456           // dataset
4457           // reference
4458           Alignment prods = CrossRef
4459                   .findXrefSequences(fsel, fdna, fsrc, ds);
4460           if (prods != null)
4461           {
4462             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4463             for (int s = 0; s < sprods.length; s++)
4464             {
4465               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4466               if (ds.getSequences() == null
4467                       || !ds.getSequences().contains(
4468                               sprods[s].getDatasetSequence()))
4469                 ds.addSequence(sprods[s].getDatasetSequence());
4470               sprods[s].updatePDBIds();
4471             }
4472             Alignment al = new Alignment(sprods);
4473             AlignedCodonFrame[] cf = prods.getCodonFrames();
4474             al.setDataset(ds);
4475             for (int s = 0; cf != null && s < cf.length; s++)
4476             {
4477               al.addCodonFrame(cf[s]);
4478               cf[s] = null;
4479             }
4480             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4481                     DEFAULT_HEIGHT);
4482             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4483                     + " for " + ((fisRegSel) ? "selected region of " : "")
4484                     + getTitle();
4485             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4486                     DEFAULT_HEIGHT);
4487           }
4488           else
4489           {
4490             System.err.println("No Sequences generated for xRef type "
4491                     + fsrc);
4492           }
4493         } catch (Exception e)
4494         {
4495           jalview.bin.Cache.log.error(
4496                   "Exception when finding crossreferences", e);
4497         } catch (OutOfMemoryError e)
4498         {
4499           new OOMWarning("whilst fetching crossreferences", e);
4500         } catch (Error e)
4501         {
4502           jalview.bin.Cache.log.error("Error when finding crossreferences",
4503                   e);
4504         }
4505         ths.setProgressBar("Finished searching for sequences from " + fsrc,
4506                 sttime);
4507       }
4508
4509     };
4510     Thread frunner = new Thread(foo);
4511     frunner.start();
4512   }
4513
4514   public boolean canShowTranslationProducts(SequenceI[] selection,
4515           AlignmentI alignment)
4516   {
4517     // old way
4518     try
4519     {
4520       return (jalview.analysis.Dna.canTranslate(selection,
4521               viewport.getViewAsVisibleContigs(true)));
4522     } catch (Exception e)
4523     {
4524       jalview.bin.Cache.log
4525               .warn("canTranslate threw an exception - please report to help@jalview.org",
4526                       e);
4527       return false;
4528     }
4529   }
4530
4531   @Override
4532   public void showProducts_actionPerformed(ActionEvent e)
4533   {
4534     // /////////////////////////////
4535     // Collect Data to be translated/transferred
4536
4537     SequenceI[] selection = viewport.getSequenceSelection();
4538     AlignmentI al = null;
4539     try
4540     {
4541       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4542               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4543               viewport.getAlignment().getDataset());
4544     } catch (Exception ex)
4545     {
4546       al = null;
4547       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4548     }
4549     if (al == null)
4550     {
4551       JOptionPane
4552               .showMessageDialog(
4553                       Desktop.desktop,
4554                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4555                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4556     }
4557     else
4558     {
4559       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4560       Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
4561               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562     }
4563   }
4564
4565   @Override
4566   public void showTranslation_actionPerformed(ActionEvent e)
4567   {
4568     // /////////////////////////////
4569     // Collect Data to be translated/transferred
4570
4571     SequenceI[] selection = viewport.getSequenceSelection();
4572     String[] seqstring = viewport.getViewAsString(true);
4573     AlignmentI al = null;
4574     try
4575     {
4576       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4577               viewport.getViewAsVisibleContigs(true), viewport
4578                       .getGapCharacter(), viewport.getAlignment()
4579                       .getAlignmentAnnotation(), viewport.getAlignment()
4580                       .getWidth(), viewport.getAlignment().getDataset());
4581     } catch (Exception ex)
4582     {
4583       al = null;
4584       jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
4585       JOptionPane
4586       .showMessageDialog(
4587               Desktop.desktop,
4588               MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
4589               MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
4590       return;
4591     }
4592     if (al == null)
4593     {
4594       JOptionPane
4595               .showMessageDialog(
4596                       Desktop.desktop,
4597                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4598                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4599     }
4600     else
4601     {
4602       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4603       Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
4604               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4605     }
4606   }
4607
4608   /**
4609    * Try to load a features file onto the alignment.
4610    *
4611    * @param file
4612    *          contents or path to retrieve file
4613    * @param type
4614    *          access mode of file (see jalview.io.AlignFile)
4615    * @return true if features file was parsed corectly.
4616    */
4617   public boolean parseFeaturesFile(String file, String type)
4618   {
4619     boolean featuresFile = false;
4620     try
4621     {
4622       featuresFile = new FeaturesFile(file, type).parse(viewport
4623               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4624               .getFeatureRenderer().featureColours, false,
4625               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4626     } catch (Exception ex)
4627     {
4628       ex.printStackTrace();
4629     }
4630
4631     if (featuresFile)
4632     {
4633       viewport.showSequenceFeatures = true;
4634       showSeqFeatures.setSelected(true);
4635       if (alignPanel.seqPanel.seqCanvas.fr != null)
4636       {
4637         // update the min/max ranges where necessary
4638         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4639       }
4640       if (featureSettings != null)
4641       {
4642         featureSettings.setTableData();
4643       }
4644       alignPanel.paintAlignment(true);
4645     }
4646
4647     return featuresFile;
4648   }
4649
4650   @Override
4651   public void dragEnter(DropTargetDragEvent evt)
4652   {
4653   }
4654
4655   @Override
4656   public void dragExit(DropTargetEvent evt)
4657   {
4658   }
4659
4660   @Override
4661   public void dragOver(DropTargetDragEvent evt)
4662   {
4663   }
4664
4665   @Override
4666   public void dropActionChanged(DropTargetDragEvent evt)
4667   {
4668   }
4669
4670   @Override
4671   public void drop(DropTargetDropEvent evt)
4672   {
4673     Transferable t = evt.getTransferable();
4674     java.util.List files = null;
4675
4676     try
4677     {
4678       DataFlavor uriListFlavor = new DataFlavor(
4679               "text/uri-list;class=java.lang.String");
4680       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4681       {
4682         // Works on Windows and MacOSX
4683         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4684         files = (java.util.List) t
4685                 .getTransferData(DataFlavor.javaFileListFlavor);
4686       }
4687       else if (t.isDataFlavorSupported(uriListFlavor))
4688       {
4689         // This is used by Unix drag system
4690         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4691         String data = (String) t.getTransferData(uriListFlavor);
4692         files = new java.util.ArrayList(1);
4693         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4694                 data, "\r\n"); st.hasMoreTokens();)
4695         {
4696           String s = st.nextToken();
4697           if (s.startsWith("#"))
4698           {
4699             // the line is a comment (as per the RFC 2483)
4700             continue;
4701           }
4702
4703           java.net.URI uri = new java.net.URI(s);
4704           // check to see if we can handle this kind of URI
4705           if (uri.getScheme().toLowerCase().startsWith("http"))
4706           {
4707             files.add(uri.toString());
4708           }
4709           else
4710           {
4711             // otherwise preserve old behaviour: catch all for file objects
4712             java.io.File file = new java.io.File(uri);
4713             files.add(file.toString());
4714           }
4715         }
4716       }
4717     } catch (Exception e)
4718     {
4719       e.printStackTrace();
4720     }
4721     if (files != null)
4722     {
4723       try
4724       {
4725         // check to see if any of these files have names matching sequences in
4726         // the alignment
4727         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4728                 .getAlignment().getSequencesArray());
4729         /**
4730          * Object[] { String,SequenceI}
4731          */
4732         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4733         ArrayList<String> filesnotmatched = new ArrayList<String>();
4734         for (int i = 0; i < files.size(); i++)
4735         {
4736           String file = files.get(i).toString();
4737           String pdbfn = "";
4738           String protocol = FormatAdapter.checkProtocol(file);
4739           if (protocol == jalview.io.FormatAdapter.FILE)
4740           {
4741             File fl = new File(file);
4742             pdbfn = fl.getName();
4743           }
4744           else if (protocol == jalview.io.FormatAdapter.URL)
4745           {
4746             URL url = new URL(file);
4747             pdbfn = url.getFile();
4748           }
4749           if (pdbfn.length() > 0)
4750           {
4751             // attempt to find a match in the alignment
4752             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4753             int l = 0, c = pdbfn.indexOf(".");
4754             while (mtch == null && c != -1)
4755             {
4756               do
4757               {
4758                 l = c;
4759               } while ((c = pdbfn.indexOf(".", l)) > l);
4760               if (l > -1)
4761               {
4762                 pdbfn = pdbfn.substring(0, l);
4763               }
4764               mtch = idm.findAllIdMatches(pdbfn);
4765             }
4766             if (mtch != null)
4767             {
4768               String type = null;
4769               try
4770               {
4771                 type = new IdentifyFile().Identify(file, protocol);
4772               } catch (Exception ex)
4773               {
4774                 type = null;
4775               }
4776               if (type != null)
4777               {
4778                 if (type.equalsIgnoreCase("PDB"))
4779                 {
4780                   filesmatched.add(new Object[]
4781                   { file, protocol, mtch });
4782                   continue;
4783                 }
4784               }
4785             }
4786             // File wasn't named like one of the sequences or wasn't a PDB file.
4787             filesnotmatched.add(file);
4788           }
4789         }
4790         int assocfiles = 0;
4791         if (filesmatched.size() > 0)
4792         {
4793           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4794                   || JOptionPane
4795                           .showConfirmDialog(
4796                                   this,
4797                                   MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
4798                                                   new String[]{Integer.valueOf(filesmatched.size()).toString()}),
4799                                   MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
4800                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4801
4802           {
4803             for (Object[] fm : filesmatched)
4804             {
4805               // try and associate
4806               // TODO: may want to set a standard ID naming formalism for
4807               // associating PDB files which have no IDs.
4808               for (SequenceI toassoc : (SequenceI[]) fm[2])
4809               {
4810                 PDBEntry pe = new AssociatePdbFileWithSeq()
4811                         .associatePdbWithSeq((String) fm[0],
4812                                 (String) fm[1], toassoc, false);
4813                 if (pe != null)
4814                 {
4815                   System.err.println("Associated file : "
4816                           + ((String) fm[0]) + " with "
4817                           + toassoc.getDisplayId(true));
4818                   assocfiles++;
4819                 }
4820               }
4821               alignPanel.paintAlignment(true);
4822             }
4823           }
4824         }
4825         if (filesnotmatched.size() > 0)
4826         {
4827           if (assocfiles > 0
4828                   && (Cache.getDefault(
4829                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4830                           .showConfirmDialog(
4831                                   this,
4832                                   MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
4833                                   MessageManager.getString("label.ignore_unmatched_dropped_files"),
4834                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4835           {
4836             return;
4837           }
4838           for (String fn : filesnotmatched)
4839           {
4840             loadJalviewDataFile(fn, null, null, null);
4841           }
4842
4843         }
4844       } catch (Exception ex)
4845       {
4846         ex.printStackTrace();
4847       }
4848     }
4849   }
4850
4851   /**
4852    * Attempt to load a "dropped" file or URL string: First by testing whether
4853    * it's and Annotation file, then a JNet file, and finally a features file. If
4854    * all are false then the user may have dropped an alignment file onto this
4855    * AlignFrame.
4856    *
4857    * @param file
4858    *          either a filename or a URL string.
4859    */
4860   public void loadJalviewDataFile(String file, String protocol,
4861           String format, SequenceI assocSeq)
4862   {
4863     try
4864     {
4865       if (protocol == null)
4866       {
4867         protocol = jalview.io.FormatAdapter.checkProtocol(file);
4868       }
4869       // if the file isn't identified, or not positively identified as some
4870       // other filetype (PFAM is default unidentified alignment file type) then
4871       // try to parse as annotation.
4872       boolean isAnnotation = (format == null || format
4873               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4874               .readAnnotationFile(viewport.getAlignment(), file, protocol)
4875               : false;
4876
4877       if (!isAnnotation)
4878       {
4879         // first see if its a T-COFFEE score file
4880         TCoffeeScoreFile tcf = null;
4881         try
4882         {
4883           tcf = new TCoffeeScoreFile(file, protocol);
4884           if (tcf.isValid())
4885           {
4886             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4887             {
4888               tcoffeeColour.setEnabled(true);
4889               tcoffeeColour.setSelected(true);
4890               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4891               isAnnotation = true;
4892               statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4893             }
4894             else
4895             {
4896               // some problem - if no warning its probable that the ID matching
4897               // process didn't work
4898               JOptionPane
4899                       .showMessageDialog(
4900                               Desktop.desktop,
4901                               tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
4902                                       : tcf.getWarningMessage(),
4903                               MessageManager.getString("label.problem_reading_tcoffee_score_file"),
4904                               JOptionPane.WARNING_MESSAGE);
4905             }
4906           }
4907           else
4908           {
4909             tcf = null;
4910           }
4911         } catch (Exception x)
4912         {
4913           Cache.log
4914                   .debug("Exception when processing data source as T-COFFEE score file",
4915                           x);
4916           tcf = null;
4917         }
4918         if (tcf == null)
4919         {
4920           // try to see if its a JNet 'concise' style annotation file *before*
4921           // we
4922           // try to parse it as a features file
4923           if (format == null)
4924           {
4925             format = new IdentifyFile().Identify(file, protocol);
4926           }
4927           if (format.equalsIgnoreCase("JnetFile"))
4928           {
4929             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4930                     file, protocol);
4931             new JnetAnnotationMaker().add_annotation(predictions,
4932                     viewport.getAlignment(), 0, false);
4933             isAnnotation = true;
4934           }
4935           else
4936           {
4937             /*
4938              * if (format.equalsIgnoreCase("PDB")) {
4939              *
4940              * String pdbfn = ""; // try to match up filename with sequence id
4941              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4942              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4943              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4944              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4945              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4946              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4947              * // attempt to find a match in the alignment SequenceI mtch =
4948              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4949              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4950              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4951              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4952              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4953              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4954              * { System.err.println("Associated file : " + file + " with " +
4955              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4956              * TODO: maybe need to load as normal otherwise return; } }
4957              */
4958             // try to parse it as a features file
4959             boolean isGroupsFile = parseFeaturesFile(file, protocol);
4960             // if it wasn't a features file then we just treat it as a general
4961             // alignment file to load into the current view.
4962             if (!isGroupsFile)
4963             {
4964               new FileLoader().LoadFile(viewport, file, protocol, format);
4965             }
4966             else
4967             {
4968               alignPanel.paintAlignment(true);
4969             }
4970           }
4971         }
4972       }
4973       if (isAnnotation)
4974       {
4975
4976         alignPanel.adjustAnnotationHeight();
4977         viewport.updateSequenceIdColours();
4978         buildSortByAnnotationScoresMenu();
4979         alignPanel.paintAlignment(true);
4980       }
4981     } catch (Exception ex)
4982     {
4983       ex.printStackTrace();
4984     } catch (OutOfMemoryError oom)
4985     {
4986       try
4987       {
4988         System.gc();
4989       } catch (Exception x)
4990       {
4991       }
4992       ;
4993       new OOMWarning(
4994               "loading data "
4995                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
4996                               : "using " + protocol + " from " + file)
4997                               : ".")
4998                       + (format != null ? "(parsing as '" + format
4999                               + "' file)" : ""), oom, Desktop.desktop);
5000     }
5001   }
5002
5003   @Override
5004   public void tabSelectionChanged(int index)
5005   {
5006     if (index > -1)
5007     {
5008       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5009       viewport = alignPanel.av;
5010       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5011       setMenusFromViewport(viewport);
5012     }
5013   }
5014
5015   @Override
5016   public void tabbedPane_mousePressed(MouseEvent e)
5017   {
5018     if (SwingUtilities.isRightMouseButton(e))
5019     {
5020       String reply = JOptionPane.showInternalInputDialog(this,
5021               MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
5022               JOptionPane.QUESTION_MESSAGE);
5023
5024       if (reply != null)
5025       {
5026         viewport.viewName = reply;
5027         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5028       }
5029     }
5030   }
5031
5032   public AlignViewport getCurrentView()
5033   {
5034     return viewport;
5035   }
5036
5037   /**
5038    * Open the dialog for regex description parsing.
5039    */
5040   @Override
5041   protected void extractScores_actionPerformed(ActionEvent e)
5042   {
5043     ParseProperties pp = new jalview.analysis.ParseProperties(
5044             viewport.getAlignment());
5045     // TODO: verify regex and introduce GUI dialog for version 2.5
5046     // if (pp.getScoresFromDescription("col", "score column ",
5047     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5048     // true)>0)
5049     if (pp.getScoresFromDescription("description column",
5050             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5051     {
5052       buildSortByAnnotationScoresMenu();
5053     }
5054   }
5055
5056   /*
5057    * (non-Javadoc)
5058    *
5059    * @see
5060    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5061    * )
5062    */
5063   @Override
5064   protected void showDbRefs_actionPerformed(ActionEvent e)
5065   {
5066     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5067   }
5068
5069   /*
5070    * (non-Javadoc)
5071    *
5072    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5073    * ActionEvent)
5074    */
5075   @Override
5076   protected void showNpFeats_actionPerformed(ActionEvent e)
5077   {
5078     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5079   }
5080
5081   /**
5082    * find the viewport amongst the tabs in this alignment frame and close that
5083    * tab
5084    *
5085    * @param av
5086    */
5087   public boolean closeView(AlignViewport av)
5088   {
5089     if (viewport == av)
5090     {
5091       this.closeMenuItem_actionPerformed(false);
5092       return true;
5093     }
5094     Component[] comp = tabbedPane.getComponents();
5095     for (int i = 0; comp != null && i < comp.length; i++)
5096     {
5097       if (comp[i] instanceof AlignmentPanel)
5098       {
5099         if (((AlignmentPanel) comp[i]).av == av)
5100         {
5101           // close the view.
5102           closeView((AlignmentPanel) comp[i]);
5103           return true;
5104         }
5105       }
5106     }
5107     return false;
5108   }
5109
5110   protected void build_fetchdbmenu(JMenu webService)
5111   {
5112     // Temporary hack - DBRef Fetcher always top level ws entry.
5113     // TODO We probably want to store a sequence database checklist in
5114     // preferences and have checkboxes.. rather than individual sources selected
5115     // here
5116     final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
5117     rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
5118     webService.add(rfetch);
5119
5120     JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
5121     fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
5122     fetchr.addActionListener(new ActionListener()
5123     {
5124
5125       @Override
5126       public void actionPerformed(ActionEvent e)
5127       {
5128         new Thread(new Runnable()
5129         {
5130
5131           @Override
5132           public void run()
5133           {
5134             new jalview.ws.DBRefFetcher(alignPanel.av
5135                     .getSequenceSelection(), alignPanel.alignFrame)
5136                     .fetchDBRefs(false);
5137           }
5138         }).start();
5139
5140       }
5141
5142     });
5143     rfetch.add(fetchr);
5144     final AlignFrame me = this;
5145     new Thread(new Runnable()
5146     {
5147       @Override
5148       public void run()
5149       {
5150         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5151                 .getSequenceFetcherSingleton(me);
5152         javax.swing.SwingUtilities.invokeLater(new Runnable()
5153         {
5154           @Override
5155           public void run()
5156           {
5157             String[] dbclasses = sf.getOrderedSupportedSources();
5158             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5159             // jalview.util.QuickSort.sort(otherdb, otherdb);
5160             List<DbSourceProxy> otherdb;
5161             JMenu dfetch = new JMenu();
5162             JMenu ifetch = new JMenu();
5163             JMenuItem fetchr = null;
5164             int comp = 0, icomp = 0, mcomp = 15;
5165             String mname = null;
5166             int dbi = 0;
5167             for (String dbclass : dbclasses)
5168             {
5169               otherdb = sf.getSourceProxy(dbclass);
5170               // add a single entry for this class, or submenu allowing 'fetch
5171               // all' or pick one
5172               if (otherdb == null || otherdb.size() < 1)
5173               {
5174                 continue;
5175               }
5176               // List<DbSourceProxy> dbs=otherdb;
5177               // otherdb=new ArrayList<DbSourceProxy>();
5178               // for (DbSourceProxy db:dbs)
5179               // {
5180               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5181               // }
5182               if (mname == null)
5183               {
5184                 mname = "From " + dbclass;
5185               }
5186               if (otherdb.size() == 1)
5187               {
5188                 final DbSourceProxy[] dassource = otherdb
5189                         .toArray(new DbSourceProxy[0]);
5190                 DbSourceProxy src = otherdb.get(0);
5191                 fetchr = new JMenuItem(src.getDbSource());
5192                 fetchr.addActionListener(new ActionListener()
5193                 {
5194
5195                   @Override
5196                   public void actionPerformed(ActionEvent e)
5197                   {
5198                     new Thread(new Runnable()
5199                     {
5200
5201                       @Override
5202                       public void run()
5203                       {
5204                         new jalview.ws.DBRefFetcher(alignPanel.av
5205                                 .getSequenceSelection(),
5206                                 alignPanel.alignFrame, dassource)
5207                                 .fetchDBRefs(false);
5208                       }
5209                     }).start();
5210                   }
5211
5212                 });
5213                 fetchr.setToolTipText("<html>"
5214                         + JvSwingUtils.wrapTooltip("Retrieve from "
5215                                 + src.getDbName()) + "<html>");
5216                 dfetch.add(fetchr);
5217                 comp++;
5218               }
5219               else
5220               {
5221                 final DbSourceProxy[] dassource = otherdb
5222                         .toArray(new DbSourceProxy[0]);
5223                 // fetch all entry
5224                 DbSourceProxy src = otherdb.get(0);
5225                 fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
5226                 fetchr.addActionListener(new ActionListener()
5227                 {
5228                   @Override
5229                   public void actionPerformed(ActionEvent e)
5230                   {
5231                     new Thread(new Runnable()
5232                     {
5233
5234                       @Override
5235                       public void run()
5236                       {
5237                         new jalview.ws.DBRefFetcher(alignPanel.av
5238                                 .getSequenceSelection(),
5239                                 alignPanel.alignFrame, dassource)
5240                                 .fetchDBRefs(false);
5241                       }
5242                     }).start();
5243                   }
5244                 });
5245
5246                 fetchr.setToolTipText("<html>"
5247                         + JvSwingUtils.wrapTooltip("Retrieve from all "
5248                                 + otherdb.size() + " sources in "
5249                                 + src.getDbSource() + "<br>First is :"
5250                                 + src.getDbName()) + "<html>");
5251                 dfetch.add(fetchr);
5252                 comp++;
5253                 // and then build the rest of the individual menus
5254                 ifetch = new JMenu("Sources from " + src.getDbSource());
5255                 icomp = 0;
5256                 String imname = null;
5257                 int i = 0;
5258                 for (DbSourceProxy sproxy : otherdb)
5259                 {
5260                   String dbname = sproxy.getDbName();
5261                   String sname = dbname.length() > 5 ? dbname.substring(0,
5262                           5) + "..." : dbname;
5263                   String msname = dbname.length() > 10 ? dbname.substring(
5264                           0, 10) + "..." : dbname;
5265                   if (imname == null)
5266                   {
5267                     imname = "from '" + sname + "'";
5268                   }
5269                   fetchr = new JMenuItem(msname);
5270                   final DbSourceProxy[] dassrc =
5271                   { sproxy };
5272                   fetchr.addActionListener(new ActionListener()
5273                   {
5274
5275                     @Override
5276                     public void actionPerformed(ActionEvent e)
5277                     {
5278                       new Thread(new Runnable()
5279                       {
5280
5281                         @Override
5282                         public void run()
5283                         {
5284                           new jalview.ws.DBRefFetcher(alignPanel.av
5285                                   .getSequenceSelection(),
5286                                   alignPanel.alignFrame, dassrc)
5287                                   .fetchDBRefs(false);
5288                         }
5289                       }).start();
5290                     }
5291
5292                   });
5293                   fetchr.setToolTipText("<html>"
5294                           + JvSwingUtils.wrapTooltip("Retrieve from "
5295                                   + dbname) + "</html>");
5296                   ifetch.add(fetchr);
5297                   ++i;
5298                   if (++icomp >= mcomp || i == (otherdb.size()))
5299                   {
5300                     ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
5301                     dfetch.add(ifetch);
5302                     ifetch = new JMenu();
5303                     imname = null;
5304                     icomp = 0;
5305                     comp++;
5306                   }
5307                 }
5308               }
5309               ++dbi;
5310               if (comp >= mcomp || dbi >= (dbclasses.length))
5311               {
5312                 dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
5313                 rfetch.add(dfetch);
5314                 dfetch = new JMenu();
5315                 mname = null;
5316                 comp = 0;
5317               }
5318             }
5319           }
5320         });
5321       }
5322     }).start();
5323
5324   }
5325
5326   /**
5327    * Left justify the whole alignment.
5328    */
5329   @Override
5330   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5331   {
5332     AlignmentI al = viewport.getAlignment();
5333     al.justify(false);
5334     viewport.firePropertyChange("alignment", null, al);
5335   }
5336
5337   /**
5338    * Right justify the whole alignment.
5339    */
5340   @Override
5341   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5342   {
5343     AlignmentI al = viewport.getAlignment();
5344     al.justify(true);
5345     viewport.firePropertyChange("alignment", null, al);
5346   }
5347
5348   public void setShowSeqFeatures(boolean b)
5349   {
5350     showSeqFeatures.setSelected(true);
5351     viewport.setShowSequenceFeatures(true);
5352   }
5353
5354   /*
5355    * (non-Javadoc)
5356    *
5357    * @see
5358    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5359    * awt.event.ActionEvent)
5360    */
5361   @Override
5362   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5363   {
5364     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5365     alignPanel.paintAlignment(true);
5366   }
5367
5368   /*
5369    * (non-Javadoc)
5370    *
5371    * @see
5372    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5373    * .ActionEvent)
5374    */
5375   @Override
5376   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5377   {
5378     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5379     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5380
5381   }
5382
5383   /*
5384    * (non-Javadoc)
5385    *
5386    * @see
5387    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5388    * .event.ActionEvent)
5389    */
5390   @Override
5391   protected void showGroupConservation_actionPerformed(ActionEvent e)
5392   {
5393     viewport.setShowGroupConservation(showGroupConservation.getState());
5394     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5395   }
5396
5397   /*
5398    * (non-Javadoc)
5399    *
5400    * @see
5401    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5402    * .event.ActionEvent)
5403    */
5404   @Override
5405   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5406   {
5407     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5408     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5409   }
5410
5411   /*
5412    * (non-Javadoc)
5413    *
5414    * @see
5415    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5416    * .event.ActionEvent)
5417    */
5418   @Override
5419   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5420   {
5421     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5422     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5423   }
5424
5425   @Override
5426   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5427   {
5428     showSequenceLogo.setState(true);
5429     viewport.setShowSequenceLogo(true);
5430     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5431     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5432   }
5433
5434   @Override
5435   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5436   {
5437     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5438   }
5439
5440   /*
5441    * (non-Javadoc)
5442    *
5443    * @see
5444    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5445    * .event.ActionEvent)
5446    */
5447   @Override
5448   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5449   {
5450     if (avc.makeGroupsFromSelection()) {
5451       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5452       alignPanel.updateAnnotation();
5453       alignPanel.paintAlignment(true);
5454     }
5455   }
5456
5457   @Override
5458   protected void createGroup_actionPerformed(ActionEvent e)
5459   {
5460     if (avc.createGroup())
5461     {
5462       alignPanel.alignmentChanged();
5463     }
5464   }
5465
5466   @Override
5467   protected void unGroup_actionPerformed(ActionEvent e)
5468   {
5469     if (avc.unGroup())
5470     {
5471       alignPanel.alignmentChanged();
5472     }
5473   }
5474
5475   /**
5476    * make the given alignmentPanel the currently selected tab
5477    *
5478    * @param alignmentPanel
5479    */
5480   public void setDisplayedView(AlignmentPanel alignmentPanel)
5481   {
5482     if (!viewport.getSequenceSetId().equals(
5483             alignmentPanel.av.getSequenceSetId()))
5484     {
5485       throw new Error(
5486               "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5487     }
5488     if (tabbedPane != null
5489             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5490                     .getSelectedIndex())
5491     {
5492       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5493     }
5494   }
5495 }
5496
5497 class PrintThread extends Thread
5498 {
5499   AlignmentPanel ap;
5500
5501   public PrintThread(AlignmentPanel ap)
5502   {
5503     this.ap = ap;
5504   }
5505
5506   static PageFormat pf;
5507
5508   @Override
5509   public void run()
5510   {
5511     PrinterJob printJob = PrinterJob.getPrinterJob();
5512
5513     if (pf != null)
5514     {
5515       printJob.setPrintable(ap, pf);
5516     }
5517     else
5518     {
5519       printJob.setPrintable(ap);
5520     }
5521
5522     if (printJob.printDialog())
5523     {
5524       try
5525       {
5526         printJob.print();
5527       } catch (Exception PrintException)
5528       {
5529         PrintException.printStackTrace();
5530       }
5531     }
5532   }
5533 }