src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Component;
  25 import java.awt.Rectangle;
  26 import java.awt.Toolkit;
  27 import java.awt.datatransfer.Clipboard;
  28 import java.awt.datatransfer.DataFlavor;
  29 import java.awt.datatransfer.StringSelection;
  30 import java.awt.datatransfer.Transferable;
  31 import java.awt.dnd.DnDConstants;
  32 import java.awt.dnd.DropTargetDragEvent;
  33 import java.awt.dnd.DropTargetDropEvent;
  34 import java.awt.dnd.DropTargetEvent;
  35 import java.awt.dnd.DropTargetListener;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.ItemEvent;
  39 import java.awt.event.ItemListener;
  40 import java.awt.event.KeyAdapter;
  41 import java.awt.event.KeyEvent;
  42 import java.awt.event.MouseAdapter;
  43 import java.awt.event.MouseEvent;
  44 import java.awt.print.PageFormat;
  45 import java.awt.print.PrinterJob;
  46 import java.beans.PropertyChangeEvent;
  47 import java.io.File;
  48 import java.net.URL;
  49 import java.util.ArrayList;
  50 import java.util.Arrays;
  51 import java.util.Deque;
  52 import java.util.Enumeration;
  53 import java.util.Hashtable;
  54 import java.util.List;
  55 import java.util.Set;
  56 import java.util.Vector;
  57
  58 import javax.swing.JCheckBoxMenuItem;
  59 import javax.swing.JEditorPane;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JLayeredPane;
  62 import javax.swing.JMenu;
  63 import javax.swing.JMenuItem;
  64 import javax.swing.JOptionPane;
  65 import javax.swing.JRadioButtonMenuItem;
  66 import javax.swing.JScrollPane;
  67 import javax.swing.SwingUtilities;
  68
  69 import jalview.analysis.AAFrequency;
  70 import jalview.analysis.AlignmentSorter;
  71 import jalview.analysis.AlignmentUtils;
  72 import jalview.analysis.Conservation;
  73 import jalview.analysis.CrossRef;
  74 import jalview.analysis.Dna;
  75 import jalview.analysis.ParseProperties;
  76 import jalview.analysis.SequenceIdMatcher;
  77 import jalview.api.AlignViewControllerGuiI;
  78 import jalview.api.AlignViewControllerI;
  79 import jalview.api.AlignViewportI;
  80 import jalview.api.AlignmentViewPanel;
  81 import jalview.api.SplitContainerI;
  82 import jalview.api.ViewStyleI;
  83 import jalview.api.analysis.ScoreModelI;
  84 import jalview.bin.Cache;
  85 import jalview.commands.CommandI;
  86 import jalview.commands.EditCommand;
  87 import jalview.commands.EditCommand.Action;
  88 import jalview.commands.OrderCommand;
  89 import jalview.commands.RemoveGapColCommand;
  90 import jalview.commands.RemoveGapsCommand;
  91 import jalview.commands.SlideSequencesCommand;
  92 import jalview.commands.TrimRegionCommand;
  93 import jalview.datamodel.AlignedCodonFrame;
  94 import jalview.datamodel.Alignment;
  95 import jalview.datamodel.AlignmentAnnotation;
  96 import jalview.datamodel.AlignmentI;
  97 import jalview.datamodel.AlignmentOrder;
  98 import jalview.datamodel.AlignmentView;
  99 import jalview.datamodel.ColumnSelection;
 100 import jalview.datamodel.HiddenSequences;
 101 import jalview.datamodel.PDBEntry;
 102 import jalview.datamodel.SeqCigar;
 103 import jalview.datamodel.Sequence;
 104 import jalview.datamodel.SequenceGroup;
 105 import jalview.datamodel.SequenceI;
 106 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 107 import jalview.io.AlignmentProperties;
 108 import jalview.io.AnnotationFile;
 109 import jalview.io.BioJsHTMLOutput;
 110 import jalview.io.FeaturesFile;
 111 import jalview.io.FileLoader;
 112 import jalview.io.FormatAdapter;
 113 import jalview.io.HtmlSvgOutput;
 114 import jalview.io.IdentifyFile;
 115 import jalview.io.JalviewFileChooser;
 116 import jalview.io.JalviewFileView;
 117 import jalview.io.JnetAnnotationMaker;
 118 import jalview.io.NewickFile;
 119 import jalview.io.TCoffeeScoreFile;
 120 import jalview.jbgui.GAlignFrame;
 121 import jalview.schemes.Blosum62ColourScheme;
 122 import jalview.schemes.BuriedColourScheme;
 123 import jalview.schemes.ClustalxColourScheme;
 124 import jalview.schemes.ColourSchemeI;
 125 import jalview.schemes.ColourSchemeProperty;
 126 import jalview.schemes.HelixColourScheme;
 127 import jalview.schemes.HydrophobicColourScheme;
 128 import jalview.schemes.NucleotideColourScheme;
 129 import jalview.schemes.PIDColourScheme;
 130 import jalview.schemes.PurinePyrimidineColourScheme;
 131 import jalview.schemes.RNAHelicesColourChooser;
 132 import jalview.schemes.ResidueProperties;
 133 import jalview.schemes.StrandColourScheme;
 134 import jalview.schemes.TCoffeeColourScheme;
 135 import jalview.schemes.TaylorColourScheme;
 136 import jalview.schemes.TurnColourScheme;
 137 import jalview.schemes.UserColourScheme;
 138 import jalview.schemes.ZappoColourScheme;
 139 import jalview.structure.StructureSelectionManager;
 140 import jalview.util.MessageManager;
 141 import jalview.viewmodel.AlignmentViewport;
 142 import jalview.ws.jws1.Discoverer;
 143 import jalview.ws.jws2.Jws2Discoverer;
 144 import jalview.ws.jws2.jabaws2.Jws2Instance;
 145 import jalview.ws.seqfetcher.DbSourceProxy;
 146
 147 /**
 148  * DOCUMENT ME!
 149  *
 150  * @author $author$
 151  * @version $Revision$
 152  */
 153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 154         IProgressIndicator, AlignViewControllerGuiI
 155 {
 156
 157   public static final int DEFAULT_WIDTH = 700;
 158
 159   public static final int DEFAULT_HEIGHT = 500;
 160
 161   /*
 162    * The currently displayed panel (selected tabbed view if more than one)
 163    */
 164   public AlignmentPanel alignPanel;
 165
 166   AlignViewport viewport;
 167
 168   public AlignViewControllerI avc;
 169
 170   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 171
 172   /**
 173    * Last format used to load or save alignments in this window
 174    */
 175   String currentFileFormat = null;
 176
 177   /**
 178    * Current filename for this alignment
 179    */
 180   String fileName = null;
 181
 182   /**
 183    * Creates a new AlignFrame object with specific width and height.
 184    *
 185    * @param al
 186    * @param width
 187    * @param height
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height)
 190   {
 191     this(al, null, width, height);
 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    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId)
 205   {
 206     this(al, null, width, height, sequenceSetId);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    * @param viewId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId, String viewId)
 221   {
 222     this(al, null, width, height, sequenceSetId, viewId);
 223   }
 224
 225   /**
 226    * new alignment window with hidden columns
 227    *
 228    * @param al
 229    *          AlignmentI
 230    * @param hiddenColumns
 231    *          ColumnSelection or null
 232    * @param width
 233    *          Width of alignment frame
 234    * @param height
 235    *          height of frame.
 236    */
 237   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 238           int width, int height)
 239   {
 240     this(al, hiddenColumns, width, height, null);
 241   }
 242
 243   /**
 244    * Create alignment frame for al with hiddenColumns, a specific width and
 245    * height, and specific sequenceId
 246    *
 247    * @param al
 248    * @param hiddenColumns
 249    * @param width
 250    * @param height
 251    * @param sequenceSetId
 252    *          (may be null)
 253    */
 254   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 255           int width, int height, String sequenceSetId)
 256   {
 257     this(al, hiddenColumns, width, height, sequenceSetId, null);
 258   }
 259
 260   /**
 261    * Create alignment frame for al with hiddenColumns, a specific width and
 262    * height, and specific sequenceId
 263    *
 264    * @param al
 265    * @param hiddenColumns
 266    * @param width
 267    * @param height
 268    * @param sequenceSetId
 269    *          (may be null)
 270    * @param viewId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 274           int width, int height, String sequenceSetId, String viewId)
 275   {
 276     setSize(width, height);
 277
 278     if (al.getDataset() == null)
 279     {
 280       al.setDataset(null);
 281     }
 282
 283     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 284
 285     alignPanel = new AlignmentPanel(this, viewport);
 286
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   /**
 293    * Make a new AlignFrame from existing alignmentPanels
 294    *
 295    * @param ap
 296    *          AlignmentPanel
 297    * @param av
 298    *          AlignViewport
 299    */
 300   public AlignFrame(AlignmentPanel ap)
 301   {
 302     viewport = ap.av;
 303     alignPanel = ap;
 304     addAlignmentPanel(ap, false);
 305     init();
 306   }
 307
 308   /**
 309    * initalise the alignframe from the underlying viewport data and the
 310    * configurations
 311    */
 312   void init()
 313   {
 314     progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 315
 316     avc = new jalview.controller.AlignViewController(this, viewport,
 317             alignPanel);
 318     if (viewport.getAlignmentConservationAnnotation() == null)
 319     {
 320       BLOSUM62Colour.setEnabled(false);
 321       conservationMenuItem.setEnabled(false);
 322       modifyConservation.setEnabled(false);
 323       // PIDColour.setEnabled(false);
 324       // abovePIDThreshold.setEnabled(false);
 325       // modifyPID.setEnabled(false);
 326     }
 327
 328     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 329             "No sort");
 330
 331     if (sortby.equals("Id"))
 332     {
 333       sortIDMenuItem_actionPerformed(null);
 334     }
 335     else if (sortby.equals("Pairwise Identity"))
 336     {
 337       sortPairwiseMenuItem_actionPerformed(null);
 338     }
 339
 340     if (Desktop.desktop != null)
 341     {
 342       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 343       addServiceListeners();
 344       setGUINucleotide(viewport.getAlignment().isNucleotide());
 345     }
 346
 347     setMenusFromViewport(viewport);
 348     buildSortByAnnotationScoresMenu();
 349     buildTreeMenu();
 350
 351     if (viewport.getWrapAlignment())
 352     {
 353       wrapMenuItem_actionPerformed(null);
 354     }
 355
 356     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 357     {
 358       this.overviewMenuItem_actionPerformed(null);
 359     }
 360
 361     addKeyListener();
 362
 363     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 364     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 365     final String menuLabel = MessageManager
 366             .getString("label.copy_format_from");
 367     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 368             new ViewSetProvider()
 369             {
 370
 371               @Override
 372               public AlignmentPanel[] getAllAlignmentPanels()
 373               {
 374                 origview.clear();
 375                 origview.add(alignPanel);
 376                 // make an array of all alignment panels except for this one
 377                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 378                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 379                 aps.remove(AlignFrame.this.alignPanel);
 380                 return aps.toArray(new AlignmentPanel[aps.size()]);
 381               }
 382             }, selviews, new ItemListener()
 383             {
 384
 385               @Override
 386               public void itemStateChanged(ItemEvent e)
 387               {
 388                 if (origview.size() > 0)
 389                 {
 390                   final AlignmentPanel ap = origview.get(0);
 391
 392                   /*
 393                    * Copy the ViewStyle of the selected panel to 'this one'.
 394                    * Don't change value of 'scaleProteinAsCdna' unless copying
 395                    * from a SplitFrame.
 396                    */
 397                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 398                           .getViewStyle();
 399                   boolean fromSplitFrame = selviews.get(0)
 400                           .getAlignViewport().getCodingComplement() != null;
 401                   if (!fromSplitFrame)
 402                   {
 403                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 404                             .getViewStyle().isScaleProteinAsCdna());
 405                   }
 406                   ap.getAlignViewport().setViewStyle(vs);
 407
 408                   /*
 409                    * Also rescale ViewStyle of SplitFrame complement if there is
 410                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 411                    * the whole ViewStyle (allow cDNA protein to have different
 412                    * fonts)
 413                    */
 414                   AlignViewportI complement = ap.getAlignViewport()
 415                           .getCodingComplement();
 416                   if (complement != null && vs.isScaleProteinAsCdna())
 417                   {
 418                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 419                     ((SplitFrame) af.getSplitViewContainer())
 420                             .adjustLayout();
 421                     af.setMenusForViewport();
 422                   }
 423
 424                   ap.updateLayout();
 425                   ap.setSelected(true);
 426                   ap.alignFrame.setMenusForViewport();
 427
 428                 }
 429               }
 430             });
 431     formatMenu.add(vsel);
 432
 433   }
 434
 435   /**
 436    * Change the filename and format for the alignment, and enable the 'reload'
 437    * button functionality.
 438    *
 439    * @param file
 440    *          valid filename
 441    * @param format
 442    *          format of file
 443    */
 444   public void setFileName(String file, String format)
 445   {
 446     fileName = file;
 447     setFileFormat(format);
 448     reload.setEnabled(true);
 449   }
 450
 451   /**
 452    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 453    * events
 454    */
 455   void addKeyListener()
 456   {
 457     addKeyListener(new KeyAdapter()
 458     {
 459       @Override
 460       public void keyPressed(KeyEvent evt)
 461       {
 462         if (viewport.cursorMode
 463                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 464                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 465                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 466                 && Character.isDigit(evt.getKeyChar()))
 467         {
 468           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 469         }
 470
 471         switch (evt.getKeyCode())
 472         {
 473
 474         case 27: // escape key
 475           deselectAllSequenceMenuItem_actionPerformed(null);
 476
 477           break;
 478
 479         case KeyEvent.VK_DOWN:
 480           if (evt.isAltDown() || !viewport.cursorMode)
 481           {
 482             moveSelectedSequences(false);
 483           }
 484           if (viewport.cursorMode)
 485           {
 486             alignPanel.getSeqPanel().moveCursor(0, 1);
 487           }
 488           break;
 489
 490         case KeyEvent.VK_UP:
 491           if (evt.isAltDown() || !viewport.cursorMode)
 492           {
 493             moveSelectedSequences(true);
 494           }
 495           if (viewport.cursorMode)
 496           {
 497             alignPanel.getSeqPanel().moveCursor(0, -1);
 498           }
 499
 500           break;
 501
 502         case KeyEvent.VK_LEFT:
 503           if (evt.isAltDown() || !viewport.cursorMode)
 504           {
 505             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 506           }
 507           else
 508           {
 509             alignPanel.getSeqPanel().moveCursor(-1, 0);
 510           }
 511
 512           break;
 513
 514         case KeyEvent.VK_RIGHT:
 515           if (evt.isAltDown() || !viewport.cursorMode)
 516           {
 517             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 518           }
 519           else
 520           {
 521             alignPanel.getSeqPanel().moveCursor(1, 0);
 522           }
 523           break;
 524
 525         case KeyEvent.VK_SPACE:
 526           if (viewport.cursorMode)
 527           {
 528             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 529                     || evt.isShiftDown() || evt.isAltDown());
 530           }
 531           break;
 532
 533         // case KeyEvent.VK_A:
 534         // if (viewport.cursorMode)
 535         // {
 536         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 537         // //System.out.println("A");
 538         // }
 539         // break;
 540         /*
 541          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 542          * System.out.println("closing bracket"); } break;
 543          */
 544         case KeyEvent.VK_DELETE:
 545         case KeyEvent.VK_BACK_SPACE:
 546           if (!viewport.cursorMode)
 547           {
 548             cut_actionPerformed(null);
 549           }
 550           else
 551           {
 552             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 553                     || evt.isShiftDown() || evt.isAltDown());
 554           }
 555
 556           break;
 557
 558         case KeyEvent.VK_S:
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().setCursorRow();
 562           }
 563           break;
 564         case KeyEvent.VK_C:
 565           if (viewport.cursorMode && !evt.isControlDown())
 566           {
 567             alignPanel.getSeqPanel().setCursorColumn();
 568           }
 569           break;
 570         case KeyEvent.VK_P:
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().setCursorPosition();
 574           }
 575           break;
 576
 577         case KeyEvent.VK_ENTER:
 578         case KeyEvent.VK_COMMA:
 579           if (viewport.cursorMode)
 580           {
 581             alignPanel.getSeqPanel().setCursorRowAndColumn();
 582           }
 583           break;
 584
 585         case KeyEvent.VK_Q:
 586           if (viewport.cursorMode)
 587           {
 588             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 589           }
 590           break;
 591         case KeyEvent.VK_M:
 592           if (viewport.cursorMode)
 593           {
 594             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 595           }
 596           break;
 597
 598         case KeyEvent.VK_F2:
 599           viewport.cursorMode = !viewport.cursorMode;
 600           statusBar.setText(MessageManager.formatMessage(
 601                   "label.keyboard_editing_mode", new String[]
 602                   { (viewport.cursorMode ? "on" : "off") }));
 603           if (viewport.cursorMode)
 604           {
 605             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 606             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 607           }
 608           alignPanel.getSeqPanel().seqCanvas.repaint();
 609           break;
 610
 611         case KeyEvent.VK_F1:
 612           try
 613           {
 614             Help.showHelpWindow();
 615           } catch (Exception ex)
 616           {
 617             ex.printStackTrace();
 618           }
 619           break;
 620         case KeyEvent.VK_H:
 621         {
 622           boolean toggleSeqs = !evt.isControlDown();
 623           boolean toggleCols = !evt.isShiftDown();
 624           toggleHiddenRegions(toggleSeqs, toggleCols);
 625           break;
 626         }
 627         case KeyEvent.VK_PAGE_UP:
 628           if (viewport.getWrapAlignment())
 629           {
 630             alignPanel.scrollUp(true);
 631           }
 632           else
 633           {
 634             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 635                     - viewport.endSeq + viewport.startSeq);
 636           }
 637           break;
 638         case KeyEvent.VK_PAGE_DOWN:
 639           if (viewport.getWrapAlignment())
 640           {
 641             alignPanel.scrollUp(false);
 642           }
 643           else
 644           {
 645             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 646                     + viewport.endSeq - viewport.startSeq);
 647           }
 648           break;
 649         }
 650       }
 651
 652       @Override
 653       public void keyReleased(KeyEvent evt)
 654       {
 655         switch (evt.getKeyCode())
 656         {
 657         case KeyEvent.VK_LEFT:
 658           if (evt.isAltDown() || !viewport.cursorMode)
 659           {
 660             viewport.firePropertyChange("alignment", null, viewport
 661                     .getAlignment().getSequences());
 662           }
 663           break;
 664
 665         case KeyEvent.VK_RIGHT:
 666           if (evt.isAltDown() || !viewport.cursorMode)
 667           {
 668             viewport.firePropertyChange("alignment", null, viewport
 669                     .getAlignment().getSequences());
 670           }
 671           break;
 672         }
 673       }
 674     });
 675   }
 676
 677   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 678   {
 679     ap.alignFrame = this;
 680     avc = new jalview.controller.AlignViewController(this, viewport,
 681             alignPanel);
 682
 683     alignPanels.add(ap);
 684
 685     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 686
 687     int aSize = alignPanels.size();
 688
 689     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 690
 691     if (aSize == 1 && ap.av.viewName == null)
 692     {
 693       this.getContentPane().add(ap, BorderLayout.CENTER);
 694     }
 695     else
 696     {
 697       if (aSize == 2)
 698       {
 699         setInitialTabVisible();
 700       }
 701
 702       expandViews.setEnabled(true);
 703       gatherViews.setEnabled(true);
 704       tabbedPane.addTab(ap.av.viewName, ap);
 705
 706       ap.setVisible(false);
 707     }
 708
 709     if (newPanel)
 710     {
 711       if (ap.av.isPadGaps())
 712       {
 713         ap.av.getAlignment().padGaps();
 714       }
 715       ap.av.updateConservation(ap);
 716       ap.av.updateConsensus(ap);
 717       ap.av.updateStrucConsensus(ap);
 718     }
 719   }
 720
 721   public void setInitialTabVisible()
 722   {
 723     expandViews.setEnabled(true);
 724     gatherViews.setEnabled(true);
 725     tabbedPane.setVisible(true);
 726     AlignmentPanel first = alignPanels.get(0);
 727     tabbedPane.addTab(first.av.viewName, first);
 728     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 729   }
 730
 731   public AlignViewport getViewport()
 732   {
 733     return viewport;
 734   }
 735
 736   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 737   private void addServiceListeners()
 738   {
 739     final java.beans.PropertyChangeListener thisListener;
 740     Desktop.instance.addJalviewPropertyChangeListener("services",
 741             thisListener = new java.beans.PropertyChangeListener()
 742             {
 743               @Override
 744               public void propertyChange(PropertyChangeEvent evt)
 745               {
 746                 // // System.out.println("Discoverer property change.");
 747                 // if (evt.getPropertyName().equals("services"))
 748                 {
 749                   SwingUtilities.invokeLater(new Runnable()
 750                   {
 751
 752                     @Override
 753                     public void run()
 754                     {
 755                       System.err
 756                               .println("Rebuild WS Menu for service change");
 757                       BuildWebServiceMenu();
 758                     }
 759
 760                   });
 761                 }
 762               }
 763             });
 764     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 765     {
 766       @Override
 767       public void internalFrameClosed(
 768               javax.swing.event.InternalFrameEvent evt)
 769       {
 770         System.out.println("deregistering discoverer listener");
 771         Desktop.instance.removeJalviewPropertyChangeListener("services",
 772                 thisListener);
 773         closeMenuItem_actionPerformed(true);
 774       };
 775     });
 776     // Finally, build the menu once to get current service state
 777     new Thread(new Runnable()
 778     {
 779       @Override
 780       public void run()
 781       {
 782         BuildWebServiceMenu();
 783       }
 784     }).start();
 785   }
 786
 787   /**
 788    * Configure menu items that vary according to whether the alignment is
 789    * nucleotide or protein
 790    *
 791    * @param nucleotide
 792    */
 793   public void setGUINucleotide(boolean nucleotide)
 794   {
 795     showTranslation.setVisible(nucleotide);
 796     conservationMenuItem.setEnabled(!nucleotide);
 797     modifyConservation.setEnabled(!nucleotide);
 798     showGroupConservation.setEnabled(!nucleotide);
 799     rnahelicesColour.setEnabled(nucleotide);
 800     purinePyrimidineColour.setEnabled(nucleotide);
 801     showComplementMenuItem.setText(MessageManager
 802             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 803     setColourSelected(jalview.bin.Cache.getDefault(
 804             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 805                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 806   }
 807
 808   /**
 809    * set up menus for the current viewport. This may be called after any
 810    * operation that affects the data in the current view (selection changed,
 811    * etc) to update the menus to reflect the new state.
 812    */
 813   public void setMenusForViewport()
 814   {
 815     setMenusFromViewport(viewport);
 816   }
 817
 818   /**
 819    * Need to call this method when tabs are selected for multiple views, or when
 820    * loading from Jalview2XML.java
 821    *
 822    * @param av
 823    *          AlignViewport
 824    */
 825   void setMenusFromViewport(AlignViewport av)
 826   {
 827     padGapsMenuitem.setSelected(av.isPadGaps());
 828     colourTextMenuItem.setSelected(av.isShowColourText());
 829     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 830     conservationMenuItem.setSelected(av.getConservationSelected());
 831     seqLimits.setSelected(av.getShowJVSuffix());
 832     idRightAlign.setSelected(av.isRightAlignIds());
 833     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 834     renderGapsMenuItem.setSelected(av.isRenderGaps());
 835     wrapMenuItem.setSelected(av.getWrapAlignment());
 836     scaleAbove.setVisible(av.getWrapAlignment());
 837     scaleLeft.setVisible(av.getWrapAlignment());
 838     scaleRight.setVisible(av.getWrapAlignment());
 839     annotationPanelMenuItem.setState(av.isShowAnnotation());
 840     /*
 841      * Show/hide annotations only enabled if annotation panel is shown
 842      */
 843     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 844     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 845     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 846     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 847     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 848     viewTextMenuItem.setSelected(av.getShowText());
 849     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 850     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 851     showGroupConservation.setSelected(av.isShowGroupConservation());
 852     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 853     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 854     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 855
 856     setColourSelected(ColourSchemeProperty.getColourName(av
 857             .getGlobalColourScheme()));
 858
 859     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 860     hiddenMarkers.setState(av.getShowHiddenMarkers());
 861     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 862     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 863     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 864     autoCalculate.setSelected(av.autoCalculateConsensus);
 865     sortByTree.setSelected(av.sortByTree);
 866     listenToViewSelections.setSelected(av.followSelection);
 867     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 868     rnahelicesColour
 869             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 870     setShowProductsEnabled();
 871     updateEditMenuBar();
 872   }
 873
 874   private IProgressIndicator progressBar;
 875
 876   /*
 877    * (non-Javadoc)
 878    *
 879    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 880    */
 881   @Override
 882   public void setProgressBar(String message, long id)
 883   {
 884     progressBar.setProgressBar(message, id);
 885   }
 886
 887   @Override
 888   public void registerHandler(final long id,
 889           final IProgressIndicatorHandler handler)
 890   {
 891     progressBar.registerHandler(id, handler);
 892   }
 893
 894   /**
 895    *
 896    * @return true if any progress bars are still active
 897    */
 898   @Override
 899   public boolean operationInProgress()
 900   {
 901     return progressBar.operationInProgress();
 902   }
 903
 904   @Override
 905   public void setStatus(String text)
 906   {
 907     statusBar.setText(text);
 908   }
 909
 910   /*
 911    * Added so Castor Mapping file can obtain Jalview Version
 912    */
 913   public String getVersion()
 914   {
 915     return jalview.bin.Cache.getProperty("VERSION");
 916   }
 917
 918   public FeatureRenderer getFeatureRenderer()
 919   {
 920     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 921   }
 922
 923   @Override
 924   public void fetchSequence_actionPerformed(ActionEvent e)
 925   {
 926     new SequenceFetcher(this);
 927   }
 928
 929   @Override
 930   public void addFromFile_actionPerformed(ActionEvent e)
 931   {
 932     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 933   }
 934
 935   @Override
 936   public void reload_actionPerformed(ActionEvent e)
 937   {
 938     if (fileName != null)
 939     {
 940       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 941       // originating file's format
 942       // TODO: work out how to recover feature settings for correct view(s) when
 943       // file is reloaded.
 944       if (currentFileFormat.equals("Jalview"))
 945       {
 946         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 947         for (int i = 0; i < frames.length; i++)
 948         {
 949           if (frames[i] instanceof AlignFrame && frames[i] != this
 950                   && ((AlignFrame) frames[i]).fileName != null
 951                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 952           {
 953             try
 954             {
 955               frames[i].setSelected(true);
 956               Desktop.instance.closeAssociatedWindows();
 957             } catch (java.beans.PropertyVetoException ex)
 958             {
 959             }
 960           }
 961
 962         }
 963         Desktop.instance.closeAssociatedWindows();
 964
 965         FileLoader loader = new FileLoader();
 966         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 967         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 968       }
 969       else
 970       {
 971         Rectangle bounds = this.getBounds();
 972
 973         FileLoader loader = new FileLoader();
 974         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 975         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 976                 protocol, currentFileFormat);
 977
 978         newframe.setBounds(bounds);
 979         if (featureSettings != null && featureSettings.isShowing())
 980         {
 981           final Rectangle fspos = featureSettings.frame.getBounds();
 982           // TODO: need a 'show feature settings' function that takes bounds -
 983           // need to refactor Desktop.addFrame
 984           newframe.featureSettings_actionPerformed(null);
 985           final FeatureSettings nfs = newframe.featureSettings;
 986           SwingUtilities.invokeLater(new Runnable()
 987           {
 988             @Override
 989             public void run()
 990             {
 991               nfs.frame.setBounds(fspos);
 992             }
 993           });
 994           this.featureSettings.close();
 995           this.featureSettings = null;
 996         }
 997         this.closeMenuItem_actionPerformed(true);
 998       }
 999     }
1000   }
1001
1002   @Override
1003   public void addFromText_actionPerformed(ActionEvent e)
1004   {
1005     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1006   }
1007
1008   @Override
1009   public void addFromURL_actionPerformed(ActionEvent e)
1010   {
1011     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1012   }
1013
1014   @Override
1015   public void save_actionPerformed(ActionEvent e)
1016   {
1017     if (fileName == null
1018             || (currentFileFormat == null || !jalview.io.FormatAdapter
1019                     .isValidIOFormat(currentFileFormat, true))
1020             || fileName.startsWith("http"))
1021     {
1022       saveAs_actionPerformed(null);
1023     }
1024     else
1025     {
1026       saveAlignment(fileName, currentFileFormat);
1027     }
1028   }
1029
1030   /**
1031    * DOCUMENT ME!
1032    *
1033    * @param e
1034    *          DOCUMENT ME!
1035    */
1036   @Override
1037   public void saveAs_actionPerformed(ActionEvent e)
1038   {
1039     JalviewFileChooser chooser = new JalviewFileChooser(
1040             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1041             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1042             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1043             currentFileFormat, false);
1044
1045     chooser.setFileView(new JalviewFileView());
1046     chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1047     chooser.setToolTipText(MessageManager.getString("action.save"));
1048
1049     int value = chooser.showSaveDialog(this);
1050
1051     if (value == JalviewFileChooser.APPROVE_OPTION)
1052     {
1053       currentFileFormat = chooser.getSelectedFormat();
1054       while (currentFileFormat == null)
1055       {
1056         JOptionPane
1057                 .showInternalMessageDialog(
1058                         Desktop.desktop,
1059                         MessageManager
1060                                 .getString("label.select_file_format_before_saving"),
1061                         MessageManager
1062                                 .getString("label.file_format_not_specified"),
1063                         JOptionPane.WARNING_MESSAGE);
1064         currentFileFormat = chooser.getSelectedFormat();
1065         value = chooser.showSaveDialog(this);
1066         if (value != JalviewFileChooser.APPROVE_OPTION)
1067         {
1068           return;
1069         }
1070       }
1071
1072       fileName = chooser.getSelectedFile().getPath();
1073
1074       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1075               currentFileFormat);
1076
1077       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1078       if (currentFileFormat.indexOf(" ") > -1)
1079       {
1080         currentFileFormat = currentFileFormat.substring(0,
1081                 currentFileFormat.indexOf(" "));
1082       }
1083       saveAlignment(fileName, currentFileFormat);
1084     }
1085   }
1086
1087   public boolean saveAlignment(String file, String format)
1088   {
1089     boolean success = true;
1090
1091     if (format.equalsIgnoreCase("Jalview"))
1092     {
1093       String shortName = title;
1094
1095       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1096       {
1097         shortName = shortName.substring(shortName
1098                 .lastIndexOf(java.io.File.separatorChar) + 1);
1099       }
1100
1101       success = new Jalview2XML().saveAlignment(this, file, shortName);
1102
1103       statusBar.setText(MessageManager.formatMessage(
1104               "label.successfully_saved_to_file_in_format", new Object[]
1105               { fileName, format }));
1106
1107     }
1108     else
1109     {
1110       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1111       {
1112         warningMessage("Cannot save file " + fileName + " using format "
1113                 + format, "Alignment output format not supported");
1114         saveAs_actionPerformed(null);
1115         // JBPNote need to have a raise_gui flag here
1116         return false;
1117       }
1118
1119       ExportData exportData = getAlignmentForExport();
1120       FormatAdapter f = new FormatAdapter(viewport);
1121       String output = f.formatSequences(format,
1122               exportData.getAlignment(), // class cast exceptions will
1123               // occur in the distant future
1124               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1125               f.getCacheSuffixDefault(format),
1126               viewport.getColumnSelection());
1127
1128       if (output == null)
1129       {
1130         success = false;
1131       }
1132       else
1133       {
1134         try
1135         {
1136           java.io.PrintWriter out = new java.io.PrintWriter(
1137                   new java.io.FileWriter(file));
1138
1139           out.print(output);
1140           out.close();
1141           this.setTitle(file);
1142           statusBar.setText(MessageManager.formatMessage(
1143                   "label.successfully_saved_to_file_in_format",
1144                   new Object[]
1145                   { fileName, format }));
1146         } catch (Exception ex)
1147         {
1148           success = false;
1149           ex.printStackTrace();
1150         }
1151       }
1152     }
1153
1154     if (!success)
1155     {
1156       JOptionPane.showInternalMessageDialog(this, MessageManager
1157               .formatMessage("label.couldnt_save_file", new Object[]
1158               { fileName }), MessageManager
1159               .getString("label.error_saving_file"),
1160               JOptionPane.WARNING_MESSAGE);
1161     }
1162
1163     return success;
1164   }
1165
1166
1167   private void warningMessage(String warning, String title)
1168   {
1169     if (new jalview.util.Platform().isHeadless())
1170     {
1171       System.err.println("Warning: " + title + "\nWarning: " + warning);
1172
1173     }
1174     else
1175     {
1176       JOptionPane.showInternalMessageDialog(this, warning, title,
1177               JOptionPane.WARNING_MESSAGE);
1178     }
1179     return;
1180   }
1181
1182   /**
1183    * DOCUMENT ME!
1184    *
1185    * @param e
1186    *          DOCUMENT ME!
1187    */
1188   @Override
1189   protected void outputText_actionPerformed(ActionEvent e)
1190   {
1191
1192     ExportData exportData = getAlignmentForExport();
1193     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1194     cap.setForInput(null);
1195
1196     try
1197     {
1198       cap.setText(new FormatAdapter(viewport).formatSequences(
1199               e.getActionCommand(),
1200  exportData.getAlignment(),
1201               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1202               viewport.getColumnSelection()));
1203       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1204               "label.alignment_output_command", new Object[]
1205               { e.getActionCommand() }), 600, 500);
1206     } catch (OutOfMemoryError oom)
1207     {
1208       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1209       cap.dispose();
1210     }
1211
1212   }
1213
1214   public ExportData getAlignmentForExport()
1215   {
1216     AlignmentI alignmentToExport = null;
1217     String[] omitHidden = null;
1218     int[] alignmentStartEnd = new int[2];
1219     FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
1220     viewport.setFeatureRenderer(fr);
1221     HiddenSequences hiddenSeqs = viewport.getAlignment()
1222             .getHiddenSequences();
1223
1224
1225     alignmentToExport = viewport.getAlignment();
1226     alignmentStartEnd = new int[]
1227     { 0, alignmentToExport.getWidth() - 1 };
1228
1229     if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
1230     {
1231       int reply = JOptionPane
1232               .showInternalConfirmDialog(
1233                       Desktop.desktop,
1234                       MessageManager
1235                               .getString("label.alignment_contains_hidden_columns"),
1236                       MessageManager
1237                               .getString("action.save_omit_hidden_columns"),
1238                       JOptionPane.YES_NO_OPTION,
1239                       JOptionPane.QUESTION_MESSAGE);
1240
1241       if (reply == JOptionPane.YES_OPTION)
1242       {
1243         // export only visible region
1244         omitHidden = viewport.getViewAsString(false);
1245         alignmentToExport = viewport.getAlignment();
1246         alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1247                 .getColumnSelection().getHiddenColumns());
1248       }
1249       else
1250       {
1251         // export all region including visible
1252         alignmentToExport = hiddenSeqs.getFullAlignment();
1253       }
1254     }
1255
1256     return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
1257   }
1258
1259   private static int[] getStartEnd(int[] aligmentStartEnd,
1260           List<int[]> hiddenCols)
1261   {
1262     int startPos = aligmentStartEnd[0];
1263     int endPos = aligmentStartEnd[1];
1264
1265     int[] lowestRange = new int[2];
1266     int[] higestRange = new int[2];
1267
1268     for (int[] hiddenCol : hiddenCols)
1269     {
1270       // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1271
1272       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1273       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1274     }
1275     // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1276     // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1277
1278     if (lowestRange[0] == 0 && lowestRange[1] == 0)
1279     {
1280       startPos = aligmentStartEnd[0];
1281     }
1282     else
1283     {
1284       startPos = lowestRange[1] + 1;
1285     }
1286
1287     if (higestRange[0] == 0 && higestRange[1] == 0)
1288     {
1289       endPos = aligmentStartEnd[1];
1290     }
1291     else
1292     {
1293       endPos = higestRange[0];
1294     }
1295
1296     // System.out.println("Export range : " + minPos + " - " + maxPos);
1297     return new int[]
1298     { startPos, endPos };
1299   }
1300
1301   public static void main(String[] args)
1302   {
1303     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1304     hiddenCols.add(new int[]
1305     { 0, 4 });
1306     hiddenCols.add(new int[]
1307     { 6, 9 });
1308     hiddenCols.add(new int[]
1309     { 11, 12 });
1310     hiddenCols.add(new int[]
1311     { 33, 33 });
1312     hiddenCols.add(new int[]
1313     { 45, 50 });
1314
1315     int[] x = getStartEnd(new int[]
1316     { 0, 50 }, hiddenCols);
1317     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1318   }
1319
1320   /**
1321    * DOCUMENT ME!
1322    *
1323    * @param e
1324    *          DOCUMENT ME!
1325    */
1326   @Override
1327   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1328   {
1329     // new HTMLOutput(alignPanel,
1330     // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
1331     // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1332     new HtmlSvgOutput(null, alignPanel);
1333   }
1334
1335   @Override
1336   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1337   {
1338     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
1339             alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1340     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1341   }
1342   public void createImageMap(File file, String image)
1343   {
1344     alignPanel.makePNGImageMap(file, image);
1345   }
1346
1347   /**
1348    * DOCUMENT ME!
1349    *
1350    * @param e
1351    *          DOCUMENT ME!
1352    */
1353   @Override
1354   public void createPNG(File f)
1355   {
1356     alignPanel.makePNG(f);
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   @Override
1366   public void createEPS(File f)
1367   {
1368     alignPanel.makeEPS(f);
1369   }
1370
1371   public void createSVG(File f)
1372   {
1373     alignPanel.makeSVG(f);
1374   }
1375   @Override
1376   public void pageSetup_actionPerformed(ActionEvent e)
1377   {
1378     PrinterJob printJob = PrinterJob.getPrinterJob();
1379     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1380   }
1381
1382   /**
1383    * DOCUMENT ME!
1384    *
1385    * @param e
1386    *          DOCUMENT ME!
1387    */
1388   @Override
1389   public void printMenuItem_actionPerformed(ActionEvent e)
1390   {
1391     // Putting in a thread avoids Swing painting problems
1392     PrintThread thread = new PrintThread(alignPanel);
1393     thread.start();
1394   }
1395
1396   @Override
1397   public void exportFeatures_actionPerformed(ActionEvent e)
1398   {
1399     new AnnotationExporter().exportFeatures(alignPanel);
1400   }
1401
1402   @Override
1403   public void exportAnnotations_actionPerformed(ActionEvent e)
1404   {
1405     new AnnotationExporter().exportAnnotations(alignPanel);
1406   }
1407
1408   @Override
1409   public void associatedData_actionPerformed(ActionEvent e)
1410   {
1411     // Pick the tree file
1412     JalviewFileChooser chooser = new JalviewFileChooser(
1413             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1414     chooser.setFileView(new JalviewFileView());
1415     chooser.setDialogTitle(MessageManager
1416             .getString("label.load_jalview_annotations"));
1417     chooser.setToolTipText(MessageManager
1418             .getString("label.load_jalview_annotations"));
1419
1420     int value = chooser.showOpenDialog(null);
1421
1422     if (value == JalviewFileChooser.APPROVE_OPTION)
1423     {
1424       String choice = chooser.getSelectedFile().getPath();
1425       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1426       loadJalviewDataFile(choice, null, null, null);
1427     }
1428
1429   }
1430
1431   /**
1432    * Close the current view or all views in the alignment frame. If the frame
1433    * only contains one view then the alignment will be removed from memory.
1434    *
1435    * @param closeAllTabs
1436    */
1437   @Override
1438   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1439   {
1440     if (alignPanels != null && alignPanels.size() < 2)
1441     {
1442       closeAllTabs = true;
1443     }
1444
1445     try
1446     {
1447       if (alignPanels != null)
1448       {
1449         if (closeAllTabs)
1450         {
1451           if (this.isClosed())
1452           {
1453             // really close all the windows - otherwise wait till
1454             // setClosed(true) is called
1455             for (int i = 0; i < alignPanels.size(); i++)
1456             {
1457               AlignmentPanel ap = alignPanels.get(i);
1458               ap.closePanel();
1459             }
1460           }
1461         }
1462         else
1463         {
1464           closeView(alignPanel);
1465         }
1466       }
1467
1468       if (closeAllTabs)
1469       {
1470         this.setClosed(true);
1471       }
1472     } catch (Exception ex)
1473     {
1474       ex.printStackTrace();
1475     }
1476   }
1477
1478   /**
1479    * Close the specified panel and close up tabs appropriately.
1480    *
1481    * @param panelToClose
1482    */
1483   public void closeView(AlignmentPanel panelToClose)
1484   {
1485     int index = tabbedPane.getSelectedIndex();
1486     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487     alignPanels.remove(panelToClose);
1488     panelToClose.closePanel();
1489     panelToClose = null;
1490
1491     tabbedPane.removeTabAt(closedindex);
1492     tabbedPane.validate();
1493
1494     if (index > closedindex || index == tabbedPane.getTabCount())
1495     {
1496       // modify currently selected tab index if necessary.
1497       index--;
1498     }
1499
1500     this.tabSelectionChanged(index);
1501   }
1502
1503   /**
1504    * DOCUMENT ME!
1505    */
1506   void updateEditMenuBar()
1507   {
1508
1509     if (viewport.getHistoryList().size() > 0)
1510     {
1511       undoMenuItem.setEnabled(true);
1512       CommandI command = viewport.getHistoryList().peek();
1513       undoMenuItem.setText(MessageManager.formatMessage(
1514               "label.undo_command", new Object[]
1515               { command.getDescription() }));
1516     }
1517     else
1518     {
1519       undoMenuItem.setEnabled(false);
1520       undoMenuItem.setText(MessageManager.getString("action.undo"));
1521     }
1522
1523     if (viewport.getRedoList().size() > 0)
1524     {
1525       redoMenuItem.setEnabled(true);
1526
1527       CommandI command = viewport.getRedoList().peek();
1528       redoMenuItem.setText(MessageManager.formatMessage(
1529               "label.redo_command", new Object[]
1530               { command.getDescription() }));
1531     }
1532     else
1533     {
1534       redoMenuItem.setEnabled(false);
1535       redoMenuItem.setText(MessageManager.getString("action.redo"));
1536     }
1537   }
1538
1539   public void addHistoryItem(CommandI command)
1540   {
1541     if (command.getSize() > 0)
1542     {
1543       viewport.addToHistoryList(command);
1544       viewport.clearRedoList();
1545       updateEditMenuBar();
1546       viewport.updateHiddenColumns();
1547       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1548       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1549       // viewport.getColumnSelection()
1550       // .getHiddenColumns().size() > 0);
1551     }
1552   }
1553
1554   /**
1555    *
1556    * @return alignment objects for all views
1557    */
1558   AlignmentI[] getViewAlignments()
1559   {
1560     if (alignPanels != null)
1561     {
1562       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1563       int i = 0;
1564       for (AlignmentPanel ap : alignPanels)
1565       {
1566         als[i++] = ap.av.getAlignment();
1567       }
1568       return als;
1569     }
1570     if (viewport != null)
1571     {
1572       return new AlignmentI[]
1573       { viewport.getAlignment() };
1574     }
1575     return null;
1576   }
1577
1578   /**
1579    * DOCUMENT ME!
1580    *
1581    * @param e
1582    *          DOCUMENT ME!
1583    */
1584   @Override
1585   protected void undoMenuItem_actionPerformed(ActionEvent e)
1586   {
1587     if (viewport.getHistoryList().isEmpty())
1588     {
1589       return;
1590     }
1591     CommandI command = viewport.getHistoryList().pop();
1592     viewport.addToRedoList(command);
1593     command.undoCommand(getViewAlignments());
1594
1595     AlignmentViewport originalSource = getOriginatingSource(command);
1596     updateEditMenuBar();
1597
1598     if (originalSource != null)
1599     {
1600       if (originalSource != viewport)
1601       {
1602         Cache.log
1603                 .warn("Implementation worry: mismatch of viewport origin for undo");
1604       }
1605       originalSource.updateHiddenColumns();
1606       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1607       // null
1608       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609       // viewport.getColumnSelection()
1610       // .getHiddenColumns().size() > 0);
1611       originalSource.firePropertyChange("alignment", null, originalSource
1612               .getAlignment().getSequences());
1613     }
1614   }
1615
1616   /**
1617    * DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   @Override
1623   protected void redoMenuItem_actionPerformed(ActionEvent e)
1624   {
1625     if (viewport.getRedoList().size() < 1)
1626     {
1627       return;
1628     }
1629
1630     CommandI command = viewport.getRedoList().pop();
1631     viewport.addToHistoryList(command);
1632     command.doCommand(getViewAlignments());
1633
1634     AlignmentViewport originalSource = getOriginatingSource(command);
1635     updateEditMenuBar();
1636
1637     if (originalSource != null)
1638     {
1639
1640       if (originalSource != viewport)
1641       {
1642         Cache.log
1643                 .warn("Implementation worry: mismatch of viewport origin for redo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null, originalSource
1652               .getAlignment().getSequences());
1653     }
1654   }
1655
1656   AlignmentViewport getOriginatingSource(CommandI command)
1657   {
1658     AlignmentViewport originalSource = null;
1659     // For sequence removal and addition, we need to fire
1660     // the property change event FROM the viewport where the
1661     // original alignment was altered
1662     AlignmentI al = null;
1663     if (command instanceof EditCommand)
1664     {
1665       EditCommand editCommand = (EditCommand) command;
1666       al = editCommand.getAlignment();
1667       List<Component> comps = PaintRefresher.components.get(viewport
1668               .getSequenceSetId());
1669
1670       for (Component comp : comps)
1671       {
1672         if (comp instanceof AlignmentPanel)
1673         {
1674           if (al == ((AlignmentPanel) comp).av.getAlignment())
1675           {
1676             originalSource = ((AlignmentPanel) comp).av;
1677             break;
1678           }
1679         }
1680       }
1681     }
1682
1683     if (originalSource == null)
1684     {
1685       // The original view is closed, we must validate
1686       // the current view against the closed view first
1687       if (al != null)
1688       {
1689         PaintRefresher.validateSequences(al, viewport.getAlignment());
1690       }
1691
1692       originalSource = viewport;
1693     }
1694
1695     return originalSource;
1696   }
1697
1698   /**
1699    * DOCUMENT ME!
1700    *
1701    * @param up
1702    *          DOCUMENT ME!
1703    */
1704   public void moveSelectedSequences(boolean up)
1705   {
1706     SequenceGroup sg = viewport.getSelectionGroup();
1707
1708     if (sg == null)
1709     {
1710       return;
1711     }
1712     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713             viewport.getHiddenRepSequences(), up);
1714     alignPanel.paintAlignment(true);
1715   }
1716
1717   synchronized void slideSequences(boolean right, int size)
1718   {
1719     List<SequenceI> sg = new ArrayList<SequenceI>();
1720     if (viewport.cursorMode)
1721     {
1722       sg.add(viewport.getAlignment().getSequenceAt(
1723               alignPanel.getSeqPanel().seqCanvas.cursorY));
1724     }
1725     else if (viewport.getSelectionGroup() != null
1726             && viewport.getSelectionGroup().getSize() != viewport
1727                     .getAlignment().getHeight())
1728     {
1729       sg = viewport.getSelectionGroup().getSequences(
1730               viewport.getHiddenRepSequences());
1731     }
1732
1733     if (sg.size() < 1)
1734     {
1735       return;
1736     }
1737
1738     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1739
1740     for (SequenceI seq : viewport.getAlignment().getSequences())
1741     {
1742       if (!sg.contains(seq))
1743       {
1744         invertGroup.add(seq);
1745       }
1746     }
1747
1748     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1749
1750     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751     for (int i = 0; i < invertGroup.size(); i++)
1752     {
1753       seqs2[i] = invertGroup.get(i);
1754     }
1755
1756     SlideSequencesCommand ssc;
1757     if (right)
1758     {
1759       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1760               size, viewport.getGapCharacter());
1761     }
1762     else
1763     {
1764       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1765               size, viewport.getGapCharacter());
1766     }
1767
1768     int groupAdjustment = 0;
1769     if (ssc.getGapsInsertedBegin() && right)
1770     {
1771       if (viewport.cursorMode)
1772       {
1773         alignPanel.getSeqPanel().moveCursor(size, 0);
1774       }
1775       else
1776       {
1777         groupAdjustment = size;
1778       }
1779     }
1780     else if (!ssc.getGapsInsertedBegin() && !right)
1781     {
1782       if (viewport.cursorMode)
1783       {
1784         alignPanel.getSeqPanel().moveCursor(-size, 0);
1785       }
1786       else
1787       {
1788         groupAdjustment = -size;
1789       }
1790     }
1791
1792     if (groupAdjustment != 0)
1793     {
1794       viewport.getSelectionGroup().setStartRes(
1795               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796       viewport.getSelectionGroup().setEndRes(
1797               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1798     }
1799
1800     boolean appendHistoryItem = false;
1801     Deque<CommandI> historyList = viewport.getHistoryList();
1802     if (historyList != null
1803             && historyList.size() > 0
1804             && historyList.peek() instanceof SlideSequencesCommand)
1805     {
1806       appendHistoryItem = ssc
1807               .appendSlideCommand((SlideSequencesCommand) historyList
1808                       .peek());
1809     }
1810
1811     if (!appendHistoryItem)
1812     {
1813       addHistoryItem(ssc);
1814     }
1815
1816     repaint();
1817   }
1818
1819   /**
1820    * DOCUMENT ME!
1821    *
1822    * @param e
1823    *          DOCUMENT ME!
1824    */
1825   @Override
1826   protected void copy_actionPerformed(ActionEvent e)
1827   {
1828     System.gc();
1829     if (viewport.getSelectionGroup() == null)
1830     {
1831       return;
1832     }
1833     // TODO: preserve the ordering of displayed alignment annotation in any
1834     // internal paste (particularly sequence associated annotation)
1835     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1836     String[] omitHidden = null;
1837
1838     if (viewport.hasHiddenColumns())
1839     {
1840       omitHidden = viewport.getViewAsString(true);
1841     }
1842
1843     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1844             omitHidden, null);
1845
1846     StringSelection ss = new StringSelection(output);
1847
1848     try
1849     {
1850       jalview.gui.Desktop.internalCopy = true;
1851       // Its really worth setting the clipboard contents
1852       // to empty before setting the large StringSelection!!
1853       Toolkit.getDefaultToolkit().getSystemClipboard()
1854               .setContents(new StringSelection(""), null);
1855
1856       Toolkit.getDefaultToolkit().getSystemClipboard()
1857               .setContents(ss, Desktop.instance);
1858     } catch (OutOfMemoryError er)
1859     {
1860       new OOMWarning("copying region", er);
1861       return;
1862     }
1863
1864     ArrayList<int[]> hiddenColumns = null;
1865     if (viewport.hasHiddenColumns())
1866     {
1867       hiddenColumns = new ArrayList<int[]>();
1868       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1869               .getSelectionGroup().getEndRes();
1870       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1871       {
1872         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1873         {
1874           hiddenColumns.add(new int[]
1875           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1876         }
1877       }
1878     }
1879
1880     Desktop.jalviewClipboard = new Object[]
1881     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1882     statusBar.setText(MessageManager.formatMessage(
1883             "label.copied_sequences_to_clipboard", new Object[]
1884             { Integer.valueOf(seqs.length).toString() }));
1885   }
1886
1887   /**
1888    * DOCUMENT ME!
1889    *
1890    * @param e
1891    *          DOCUMENT ME!
1892    */
1893   @Override
1894   protected void pasteNew_actionPerformed(ActionEvent e)
1895   {
1896     paste(true);
1897   }
1898
1899   /**
1900    * DOCUMENT ME!
1901    *
1902    * @param e
1903    *          DOCUMENT ME!
1904    */
1905   @Override
1906   protected void pasteThis_actionPerformed(ActionEvent e)
1907   {
1908     paste(false);
1909   }
1910
1911   /**
1912    * Paste contents of Jalview clipboard
1913    *
1914    * @param newAlignment
1915    *          true to paste to a new alignment, otherwise add to this.
1916    */
1917   void paste(boolean newAlignment)
1918   {
1919     boolean externalPaste = true;
1920     try
1921     {
1922       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1923       Transferable contents = c.getContents(this);
1924
1925       if (contents == null)
1926       {
1927         return;
1928       }
1929
1930       String str, format;
1931       try
1932       {
1933         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1934         if (str.length() < 1)
1935         {
1936           return;
1937         }
1938
1939         format = new IdentifyFile().Identify(str, "Paste");
1940
1941       } catch (OutOfMemoryError er)
1942       {
1943         new OOMWarning("Out of memory pasting sequences!!", er);
1944         return;
1945       }
1946
1947       SequenceI[] sequences;
1948       boolean annotationAdded = false;
1949       AlignmentI alignment = null;
1950
1951       if (Desktop.jalviewClipboard != null)
1952       {
1953         // The clipboard was filled from within Jalview, we must use the
1954         // sequences
1955         // And dataset from the copied alignment
1956         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1957         // be doubly sure that we create *new* sequence objects.
1958         sequences = new SequenceI[newseq.length];
1959         for (int i = 0; i < newseq.length; i++)
1960         {
1961           sequences[i] = new Sequence(newseq[i]);
1962         }
1963         alignment = new Alignment(sequences);
1964         externalPaste = false;
1965       }
1966       else
1967       {
1968         // parse the clipboard as an alignment.
1969         alignment = new FormatAdapter().readFile(str, "Paste", format);
1970         sequences = alignment.getSequencesArray();
1971       }
1972
1973       int alwidth = 0;
1974       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1975       int fgroup = -1;
1976
1977       if (newAlignment)
1978       {
1979
1980         if (Desktop.jalviewClipboard != null)
1981         {
1982           // dataset is inherited
1983           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1984         }
1985         else
1986         {
1987           // new dataset is constructed
1988           alignment.setDataset(null);
1989         }
1990         alwidth = alignment.getWidth() + 1;
1991       }
1992       else
1993       {
1994         AlignmentI pastedal = alignment; // preserve pasted alignment object
1995         // Add pasted sequences and dataset into existing alignment.
1996         alignment = viewport.getAlignment();
1997         alwidth = alignment.getWidth() + 1;
1998         // decide if we need to import sequences from an existing dataset
1999         boolean importDs = Desktop.jalviewClipboard != null
2000                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2001         // importDs==true instructs us to copy over new dataset sequences from
2002         // an existing alignment
2003         Vector newDs = (importDs) ? new Vector() : null; // used to create
2004         // minimum dataset set
2005
2006         for (int i = 0; i < sequences.length; i++)
2007         {
2008           if (importDs)
2009           {
2010             newDs.addElement(null);
2011           }
2012           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2013           // paste
2014           if (importDs && ds != null)
2015           {
2016             if (!newDs.contains(ds))
2017             {
2018               newDs.setElementAt(ds, i);
2019               ds = new Sequence(ds);
2020               // update with new dataset sequence
2021               sequences[i].setDatasetSequence(ds);
2022             }
2023             else
2024             {
2025               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2026             }
2027           }
2028           else
2029           {
2030             // copy and derive new dataset sequence
2031             sequences[i] = sequences[i].deriveSequence();
2032             alignment.getDataset().addSequence(
2033                     sequences[i].getDatasetSequence());
2034             // TODO: avoid creation of duplicate dataset sequences with a
2035             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2036           }
2037           alignment.addSequence(sequences[i]); // merges dataset
2038         }
2039         if (newDs != null)
2040         {
2041           newDs.clear(); // tidy up
2042         }
2043         if (alignment.getAlignmentAnnotation() != null)
2044         {
2045           for (AlignmentAnnotation alan : alignment
2046                   .getAlignmentAnnotation())
2047           {
2048             if (alan.graphGroup > fgroup)
2049             {
2050               fgroup = alan.graphGroup;
2051             }
2052           }
2053         }
2054         if (pastedal.getAlignmentAnnotation() != null)
2055         {
2056           // Add any annotation attached to alignment.
2057           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2058           for (int i = 0; i < alann.length; i++)
2059           {
2060             annotationAdded = true;
2061             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2062             {
2063               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2064               if (newann.graphGroup > -1)
2065               {
2066                 if (newGraphGroups.size() <= newann.graphGroup
2067                         || newGraphGroups.get(newann.graphGroup) == null)
2068                 {
2069                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2070                   {
2071                     newGraphGroups.add(q, null);
2072                   }
2073                   newGraphGroups.set(newann.graphGroup, new Integer(
2074                           ++fgroup));
2075                 }
2076                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2077                         .intValue();
2078               }
2079
2080               newann.padAnnotation(alwidth);
2081               alignment.addAnnotation(newann);
2082             }
2083           }
2084         }
2085       }
2086       if (!newAlignment)
2087       {
2088         // /////
2089         // ADD HISTORY ITEM
2090         //
2091         addHistoryItem(new EditCommand(
2092                 MessageManager.getString("label.add_sequences"),
2093                 Action.PASTE,
2094                 sequences, 0, alignment.getWidth(), alignment));
2095       }
2096       // Add any annotations attached to sequences
2097       for (int i = 0; i < sequences.length; i++)
2098       {
2099         if (sequences[i].getAnnotation() != null)
2100         {
2101           AlignmentAnnotation newann;
2102           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2103           {
2104             annotationAdded = true;
2105             newann = sequences[i].getAnnotation()[a];
2106             newann.adjustForAlignment();
2107             newann.padAnnotation(alwidth);
2108             if (newann.graphGroup > -1)
2109             {
2110               if (newann.graphGroup > -1)
2111               {
2112                 if (newGraphGroups.size() <= newann.graphGroup
2113                         || newGraphGroups.get(newann.graphGroup) == null)
2114                 {
2115                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2116                   {
2117                     newGraphGroups.add(q, null);
2118                   }
2119                   newGraphGroups.set(newann.graphGroup, new Integer(
2120                           ++fgroup));
2121                 }
2122                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2123                         .intValue();
2124               }
2125             }
2126             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2127             // was
2128             // duplicated
2129             // earlier
2130             alignment
2131                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2132           }
2133         }
2134       }
2135       if (!newAlignment)
2136       {
2137
2138         // propagate alignment changed.
2139         viewport.setEndSeq(alignment.getHeight());
2140         if (annotationAdded)
2141         {
2142           // Duplicate sequence annotation in all views.
2143           AlignmentI[] alview = this.getViewAlignments();
2144           for (int i = 0; i < sequences.length; i++)
2145           {
2146             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2147             if (sann == null)
2148             {
2149               continue;
2150             }
2151             for (int avnum = 0; avnum < alview.length; avnum++)
2152             {
2153               if (alview[avnum] != alignment)
2154               {
2155                 // duplicate in a view other than the one with input focus
2156                 int avwidth = alview[avnum].getWidth() + 1;
2157                 // this relies on sann being preserved after we
2158                 // modify the sequence's annotation array for each duplication
2159                 for (int a = 0; a < sann.length; a++)
2160                 {
2161                   AlignmentAnnotation newann = new AlignmentAnnotation(
2162                           sann[a]);
2163                   sequences[i].addAlignmentAnnotation(newann);
2164                   newann.padAnnotation(avwidth);
2165                   alview[avnum].addAnnotation(newann); // annotation was
2166                   // duplicated earlier
2167                   // TODO JAL-1145 graphGroups are not updated for sequence
2168                   // annotation added to several views. This may cause
2169                   // strangeness
2170                   alview[avnum].setAnnotationIndex(newann, a);
2171                 }
2172               }
2173             }
2174           }
2175           buildSortByAnnotationScoresMenu();
2176         }
2177         viewport.firePropertyChange("alignment", null,
2178                 alignment.getSequences());
2179         if (alignPanels != null)
2180         {
2181           for (AlignmentPanel ap : alignPanels)
2182           {
2183             ap.validateAnnotationDimensions(false);
2184           }
2185         }
2186         else
2187         {
2188           alignPanel.validateAnnotationDimensions(false);
2189         }
2190
2191       }
2192       else
2193       {
2194         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2195                 DEFAULT_HEIGHT);
2196         String newtitle = new String("Copied sequences");
2197
2198         if (Desktop.jalviewClipboard != null
2199                 && Desktop.jalviewClipboard[2] != null)
2200         {
2201           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2202           for (int[] region : hc)
2203           {
2204             af.viewport.hideColumns(region[0], region[1]);
2205           }
2206         }
2207
2208         // >>>This is a fix for the moment, until a better solution is
2209         // found!!<<<
2210         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2211                 .transferSettings(
2212                         alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2213
2214         // TODO: maintain provenance of an alignment, rather than just make the
2215         // title a concatenation of operations.
2216         if (!externalPaste)
2217         {
2218           if (title.startsWith("Copied sequences"))
2219           {
2220             newtitle = title;
2221           }
2222           else
2223           {
2224             newtitle = newtitle.concat("- from " + title);
2225           }
2226         }
2227         else
2228         {
2229           newtitle = new String("Pasted sequences");
2230         }
2231
2232         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2233                 DEFAULT_HEIGHT);
2234
2235       }
2236
2237     } catch (Exception ex)
2238     {
2239       ex.printStackTrace();
2240       System.out.println("Exception whilst pasting: " + ex);
2241       // could be anything being pasted in here
2242     }
2243
2244   }
2245
2246   @Override
2247   protected void expand_newalign(ActionEvent e)
2248   {
2249     try
2250     {
2251       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2252               .getAlignment(), -1);
2253       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2254               DEFAULT_HEIGHT);
2255       String newtitle = new String("Flanking alignment");
2256
2257       if (Desktop.jalviewClipboard != null
2258               && Desktop.jalviewClipboard[2] != null)
2259       {
2260         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2261         for (int region[] : hc)
2262         {
2263           af.viewport.hideColumns(region[0], region[1]);
2264         }
2265       }
2266
2267       // >>>This is a fix for the moment, until a better solution is
2268       // found!!<<<
2269       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2270               .transferSettings(
2271                       alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2272
2273       // TODO: maintain provenance of an alignment, rather than just make the
2274       // title a concatenation of operations.
2275       {
2276         if (title.startsWith("Copied sequences"))
2277         {
2278           newtitle = title;
2279         }
2280         else
2281         {
2282           newtitle = newtitle.concat("- from " + title);
2283         }
2284       }
2285
2286       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2287
2288     } catch (Exception ex)
2289     {
2290       ex.printStackTrace();
2291       System.out.println("Exception whilst pasting: " + ex);
2292       // could be anything being pasted in here
2293     } catch (OutOfMemoryError oom)
2294     {
2295       new OOMWarning("Viewing flanking region of alignment", oom);
2296     }
2297   }
2298
2299   /**
2300    * DOCUMENT ME!
2301    *
2302    * @param e
2303    *          DOCUMENT ME!
2304    */
2305   @Override
2306   protected void cut_actionPerformed(ActionEvent e)
2307   {
2308     copy_actionPerformed(null);
2309     delete_actionPerformed(null);
2310   }
2311
2312   /**
2313    * DOCUMENT ME!
2314    *
2315    * @param e
2316    *          DOCUMENT ME!
2317    */
2318   @Override
2319   protected void delete_actionPerformed(ActionEvent evt)
2320   {
2321
2322     SequenceGroup sg = viewport.getSelectionGroup();
2323     if (sg == null)
2324     {
2325       return;
2326     }
2327
2328     /*
2329      * If the cut affects all sequences, warn, remove highlighted columns
2330      */
2331     if (sg.getSize() == viewport.getAlignment().getHeight())
2332     {
2333       int confirm = JOptionPane.showConfirmDialog(this,
2334               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2335               MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2336               JOptionPane.OK_CANCEL_OPTION);
2337
2338       if (confirm == JOptionPane.CANCEL_OPTION
2339               || confirm == JOptionPane.CLOSED_OPTION)
2340       {
2341         return;
2342       }
2343       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2344               sg.getEndRes() + 1);
2345     }
2346
2347     SequenceI[] cut = sg.getSequences()
2348             .toArray(new SequenceI[sg.getSize()]);
2349
2350     addHistoryItem(new EditCommand(
2351             MessageManager.getString("label.cut_sequences"), Action.CUT,
2352             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2353             viewport.getAlignment()));
2354
2355     viewport.setSelectionGroup(null);
2356     viewport.sendSelection();
2357     viewport.getAlignment().deleteGroup(sg);
2358
2359     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2360             .getSequences());
2361     if (viewport.getAlignment().getHeight() < 1)
2362     {
2363       try
2364       {
2365         this.setClosed(true);
2366       } catch (Exception ex)
2367       {
2368       }
2369     }
2370   }
2371
2372   /**
2373    * DOCUMENT ME!
2374    *
2375    * @param e
2376    *          DOCUMENT ME!
2377    */
2378   @Override
2379   protected void deleteGroups_actionPerformed(ActionEvent e)
2380   {
2381     if (avc.deleteGroups())
2382     {
2383       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2384       alignPanel.updateAnnotation();
2385       alignPanel.paintAlignment(true);
2386     }
2387   }
2388
2389   /**
2390    * DOCUMENT ME!
2391    *
2392    * @param e
2393    *          DOCUMENT ME!
2394    */
2395   @Override
2396   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2397   {
2398     SequenceGroup sg = new SequenceGroup();
2399
2400     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2401     {
2402       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2403     }
2404
2405     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2406     viewport.setSelectionGroup(sg);
2407     viewport.sendSelection();
2408     alignPanel.paintAlignment(true);
2409     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2410   }
2411
2412   /**
2413    * DOCUMENT ME!
2414    *
2415    * @param e
2416    *          DOCUMENT ME!
2417    */
2418   @Override
2419   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2420   {
2421     if (viewport.cursorMode)
2422     {
2423       alignPanel.getSeqPanel().keyboardNo1 = null;
2424       alignPanel.getSeqPanel().keyboardNo2 = null;
2425     }
2426     viewport.setSelectionGroup(null);
2427     viewport.getColumnSelection().clear();
2428     viewport.setSelectionGroup(null);
2429     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2430     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2431     alignPanel.paintAlignment(true);
2432     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2433     viewport.sendSelection();
2434   }
2435
2436   /**
2437    * DOCUMENT ME!
2438    *
2439    * @param e
2440    *          DOCUMENT ME!
2441    */
2442   @Override
2443   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2444   {
2445     SequenceGroup sg = viewport.getSelectionGroup();
2446
2447     if (sg == null)
2448     {
2449       selectAllSequenceMenuItem_actionPerformed(null);
2450
2451       return;
2452     }
2453
2454     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2455     {
2456       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2457     }
2458
2459     alignPanel.paintAlignment(true);
2460     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461     viewport.sendSelection();
2462   }
2463
2464   @Override
2465   public void invertColSel_actionPerformed(ActionEvent e)
2466   {
2467     viewport.invertColumnSelection();
2468     alignPanel.paintAlignment(true);
2469     viewport.sendSelection();
2470   }
2471
2472   /**
2473    * DOCUMENT ME!
2474    *
2475    * @param e
2476    *          DOCUMENT ME!
2477    */
2478   @Override
2479   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2480   {
2481     trimAlignment(true);
2482   }
2483
2484   /**
2485    * DOCUMENT ME!
2486    *
2487    * @param e
2488    *          DOCUMENT ME!
2489    */
2490   @Override
2491   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2492   {
2493     trimAlignment(false);
2494   }
2495
2496   void trimAlignment(boolean trimLeft)
2497   {
2498     ColumnSelection colSel = viewport.getColumnSelection();
2499     int column;
2500
2501     if (colSel.size() > 0)
2502     {
2503       if (trimLeft)
2504       {
2505         column = colSel.getMin();
2506       }
2507       else
2508       {
2509         column = colSel.getMax();
2510       }
2511
2512       SequenceI[] seqs;
2513       if (viewport.getSelectionGroup() != null)
2514       {
2515         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2516                 viewport.getHiddenRepSequences());
2517       }
2518       else
2519       {
2520         seqs = viewport.getAlignment().getSequencesArray();
2521       }
2522
2523       TrimRegionCommand trimRegion;
2524       if (trimLeft)
2525       {
2526         trimRegion = new TrimRegionCommand("Remove Left",
2527                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2528                 viewport.getAlignment(), viewport.getColumnSelection(),
2529                 viewport.getSelectionGroup());
2530         viewport.setStartRes(0);
2531       }
2532       else
2533       {
2534         trimRegion = new TrimRegionCommand("Remove Right",
2535                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2536                 viewport.getAlignment(), viewport.getColumnSelection(),
2537                 viewport.getSelectionGroup());
2538       }
2539
2540       statusBar.setText(MessageManager.formatMessage(
2541               "label.removed_columns", new String[]
2542               { Integer.valueOf(trimRegion.getSize()).toString() }));
2543
2544       addHistoryItem(trimRegion);
2545
2546       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2547       {
2548         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2549                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2550         {
2551           viewport.getAlignment().deleteGroup(sg);
2552         }
2553       }
2554
2555       viewport.firePropertyChange("alignment", null, viewport
2556               .getAlignment().getSequences());
2557     }
2558   }
2559
2560   /**
2561    * DOCUMENT ME!
2562    *
2563    * @param e
2564    *          DOCUMENT ME!
2565    */
2566   @Override
2567   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2568   {
2569     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2570
2571     SequenceI[] seqs;
2572     if (viewport.getSelectionGroup() != null)
2573     {
2574       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2575               viewport.getHiddenRepSequences());
2576       start = viewport.getSelectionGroup().getStartRes();
2577       end = viewport.getSelectionGroup().getEndRes();
2578     }
2579     else
2580     {
2581       seqs = viewport.getAlignment().getSequencesArray();
2582     }
2583
2584     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2585             "Remove Gapped Columns", seqs, start, end,
2586             viewport.getAlignment());
2587
2588     addHistoryItem(removeGapCols);
2589
2590     statusBar.setText(MessageManager.formatMessage(
2591             "label.removed_empty_columns", new Object[]
2592             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2593
2594     // This is to maintain viewport position on first residue
2595     // of first sequence
2596     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2597     int startRes = seq.findPosition(viewport.startRes);
2598     // ShiftList shifts;
2599     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2600     // edit.alColumnChanges=shifts.getInverse();
2601     // if (viewport.hasHiddenColumns)
2602     // viewport.getColumnSelection().compensateForEdits(shifts);
2603     viewport.setStartRes(seq.findIndex(startRes) - 1);
2604     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2605             .getSequences());
2606
2607   }
2608
2609   /**
2610    * DOCUMENT ME!
2611    *
2612    * @param e
2613    *          DOCUMENT ME!
2614    */
2615   @Override
2616   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2617   {
2618     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2619
2620     SequenceI[] seqs;
2621     if (viewport.getSelectionGroup() != null)
2622     {
2623       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2624               viewport.getHiddenRepSequences());
2625       start = viewport.getSelectionGroup().getStartRes();
2626       end = viewport.getSelectionGroup().getEndRes();
2627     }
2628     else
2629     {
2630       seqs = viewport.getAlignment().getSequencesArray();
2631     }
2632
2633     // This is to maintain viewport position on first residue
2634     // of first sequence
2635     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2636     int startRes = seq.findPosition(viewport.startRes);
2637
2638     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2639             viewport.getAlignment()));
2640
2641     viewport.setStartRes(seq.findIndex(startRes) - 1);
2642
2643     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2644             .getSequences());
2645
2646   }
2647
2648   /**
2649    * DOCUMENT ME!
2650    *
2651    * @param e
2652    *          DOCUMENT ME!
2653    */
2654   @Override
2655   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2656   {
2657     viewport.setPadGaps(padGapsMenuitem.isSelected());
2658     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2659             .getSequences());
2660   }
2661
2662   /**
2663    * DOCUMENT ME!
2664    *
2665    * @param e
2666    *          DOCUMENT ME!
2667    */
2668   @Override
2669   public void findMenuItem_actionPerformed(ActionEvent e)
2670   {
2671     new Finder();
2672   }
2673
2674   /**
2675    * Create a new view of the current alignment.
2676    */
2677   @Override
2678   public void newView_actionPerformed(ActionEvent e)
2679   {
2680     newView(null, true);
2681   }
2682
2683   /**
2684    * Creates and shows a new view of the current alignment.
2685    *
2686    * @param viewTitle
2687    *          title of newly created view; if null, one will be generated
2688    * @param copyAnnotation
2689    *          if true then duplicate all annnotation, groups and settings
2690    * @return new alignment panel, already displayed.
2691    */
2692   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2693   {
2694     /*
2695      * Create a new AlignmentPanel (with its own, new Viewport)
2696      */
2697     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2698             true);
2699     if (!copyAnnotation)
2700     {
2701       /*
2702        * remove all groups and annotation except for the automatic stuff
2703        */
2704       newap.av.getAlignment().deleteAllGroups();
2705       newap.av.getAlignment().deleteAllAnnotations(false);
2706     }
2707
2708     newap.av.setGatherViewsHere(false);
2709
2710     if (viewport.viewName == null)
2711     {
2712       viewport.viewName = MessageManager
2713               .getString("label.view_name_original");
2714     }
2715
2716     /*
2717      * Views share the same edits, undo and redo stacks, mappings.
2718      */
2719     newap.av.setHistoryList(viewport.getHistoryList());
2720     newap.av.setRedoList(viewport.getRedoList());
2721     newap.av.getAlignment().setCodonFrames(
2722             viewport.getAlignment().getCodonFrames());
2723
2724     newap.av.viewName = getNewViewName(viewTitle);
2725
2726     addAlignmentPanel(newap, true);
2727     newap.alignmentChanged();
2728
2729     if (alignPanels.size() == 2)
2730     {
2731       viewport.setGatherViewsHere(true);
2732     }
2733     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2734     return newap;
2735   }
2736
2737   /**
2738    * Make a new name for the view, ensuring it is unique within the current
2739    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2740    * these now use viewId. Unique view names are still desirable for usability.)
2741    *
2742    * @param viewTitle
2743    * @return
2744    */
2745   protected String getNewViewName(String viewTitle)
2746   {
2747     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2748     boolean addFirstIndex = false;
2749     if (viewTitle == null || viewTitle.trim().length() == 0)
2750     {
2751       viewTitle = MessageManager.getString("action.view");
2752       addFirstIndex = true;
2753     }
2754     else
2755     {
2756       index = 1;// we count from 1 if given a specific name
2757     }
2758     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2759
2760     List<Component> comps = PaintRefresher.components.get(viewport
2761             .getSequenceSetId());
2762
2763     List<String> existingNames = getExistingViewNames(comps);
2764
2765     while (existingNames.contains(newViewName))
2766     {
2767       newViewName = viewTitle + " " + (++index);
2768     }
2769     return newViewName;
2770   }
2771
2772   /**
2773    * Returns a list of distinct view names found in the given list of
2774    * components. View names are held on the viewport of an AlignmentPanel.
2775    *
2776    * @param comps
2777    * @return
2778    */
2779   protected List<String> getExistingViewNames(List<Component> comps)
2780   {
2781     List<String> existingNames = new ArrayList<String>();
2782     for (Component comp : comps)
2783     {
2784       if (comp instanceof AlignmentPanel)
2785       {
2786         AlignmentPanel ap = (AlignmentPanel) comp;
2787         if (!existingNames.contains(ap.av.viewName))
2788         {
2789           existingNames.add(ap.av.viewName);
2790         }
2791       }
2792     }
2793     return existingNames;
2794   }
2795
2796   /**
2797    * Explode tabbed views into separate windows.
2798    */
2799   @Override
2800   public void expandViews_actionPerformed(ActionEvent e)
2801   {
2802     Desktop.instance.explodeViews(this);
2803   }
2804
2805   /**
2806    * Gather views in separate windows back into a tabbed presentation.
2807    */
2808   @Override
2809   public void gatherViews_actionPerformed(ActionEvent e)
2810   {
2811     Desktop.instance.gatherViews(this);
2812   }
2813
2814   /**
2815    * DOCUMENT ME!
2816    *
2817    * @param e
2818    *          DOCUMENT ME!
2819    */
2820   @Override
2821   public void font_actionPerformed(ActionEvent e)
2822   {
2823     new FontChooser(alignPanel);
2824   }
2825
2826   /**
2827    * DOCUMENT ME!
2828    *
2829    * @param e
2830    *          DOCUMENT ME!
2831    */
2832   @Override
2833   protected void seqLimit_actionPerformed(ActionEvent e)
2834   {
2835     viewport.setShowJVSuffix(seqLimits.isSelected());
2836
2837     alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2838             .calculateIdWidth());
2839     alignPanel.paintAlignment(true);
2840   }
2841
2842   @Override
2843   public void idRightAlign_actionPerformed(ActionEvent e)
2844   {
2845     viewport.setRightAlignIds(idRightAlign.isSelected());
2846     alignPanel.paintAlignment(true);
2847   }
2848
2849   @Override
2850   public void centreColumnLabels_actionPerformed(ActionEvent e)
2851   {
2852     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2853     alignPanel.paintAlignment(true);
2854   }
2855
2856   /*
2857    * (non-Javadoc)
2858    *
2859    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2860    */
2861   @Override
2862   protected void followHighlight_actionPerformed()
2863   {
2864     /*
2865      * Set the 'follow' flag on the Viewport (and scroll to position if now
2866      * true).
2867      */
2868     final boolean state = this.followHighlightMenuItem.getState();
2869     viewport.setFollowHighlight(state);
2870     if (state)
2871     {
2872       alignPanel.scrollToPosition(
2873               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2874     }
2875   }
2876
2877   /**
2878    * DOCUMENT ME!
2879    *
2880    * @param e
2881    *          DOCUMENT ME!
2882    */
2883   @Override
2884   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2885   {
2886     viewport.setColourText(colourTextMenuItem.isSelected());
2887     alignPanel.paintAlignment(true);
2888   }
2889
2890   /**
2891    * DOCUMENT ME!
2892    *
2893    * @param e
2894    *          DOCUMENT ME!
2895    */
2896   @Override
2897   public void wrapMenuItem_actionPerformed(ActionEvent e)
2898   {
2899     scaleAbove.setVisible(wrapMenuItem.isSelected());
2900     scaleLeft.setVisible(wrapMenuItem.isSelected());
2901     scaleRight.setVisible(wrapMenuItem.isSelected());
2902     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2903     alignPanel.updateLayout();
2904   }
2905
2906   @Override
2907   public void showAllSeqs_actionPerformed(ActionEvent e)
2908   {
2909     viewport.showAllHiddenSeqs();
2910   }
2911
2912   @Override
2913   public void showAllColumns_actionPerformed(ActionEvent e)
2914   {
2915     viewport.showAllHiddenColumns();
2916     repaint();
2917   }
2918
2919   @Override
2920   public void hideSelSequences_actionPerformed(ActionEvent e)
2921   {
2922     viewport.hideAllSelectedSeqs();
2923 //    alignPanel.paintAlignment(true);
2924   }
2925
2926   /**
2927    * called by key handler and the hide all/show all menu items
2928    *
2929    * @param toggleSeqs
2930    * @param toggleCols
2931    */
2932   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2933   {
2934
2935     boolean hide = false;
2936     SequenceGroup sg = viewport.getSelectionGroup();
2937     if (!toggleSeqs && !toggleCols)
2938     {
2939       // Hide everything by the current selection - this is a hack - we do the
2940       // invert and then hide
2941       // first check that there will be visible columns after the invert.
2942       if ((viewport.getColumnSelection() != null
2943               && viewport.getColumnSelection().getSelected() != null && viewport
2944               .getColumnSelection().getSelected().size() > 0)
2945               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2946                       .getEndRes()))
2947       {
2948         // now invert the sequence set, if required - empty selection implies
2949         // that no hiding is required.
2950         if (sg != null)
2951         {
2952           invertSequenceMenuItem_actionPerformed(null);
2953           sg = viewport.getSelectionGroup();
2954           toggleSeqs = true;
2955
2956         }
2957         viewport.expandColSelection(sg, true);
2958         // finally invert the column selection and get the new sequence
2959         // selection.
2960         invertColSel_actionPerformed(null);
2961         toggleCols = true;
2962       }
2963     }
2964
2965     if (toggleSeqs)
2966     {
2967       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2968       {
2969         hideSelSequences_actionPerformed(null);
2970         hide = true;
2971       }
2972       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2973               .size() > 0))
2974       {
2975         showAllSeqs_actionPerformed(null);
2976       }
2977     }
2978
2979     if (toggleCols)
2980     {
2981       if (viewport.getColumnSelection().getSelected().size() > 0)
2982       {
2983         hideSelColumns_actionPerformed(null);
2984         if (!toggleSeqs)
2985         {
2986           viewport.setSelectionGroup(sg);
2987         }
2988       }
2989       else if (!hide)
2990       {
2991         showAllColumns_actionPerformed(null);
2992       }
2993     }
2994   }
2995
2996   /*
2997    * (non-Javadoc)
2998    *
2999    * @see
3000    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3001    * event.ActionEvent)
3002    */
3003   @Override
3004   public void hideAllButSelection_actionPerformed(ActionEvent e)
3005   {
3006     toggleHiddenRegions(false, false);
3007   }
3008
3009   /*
3010    * (non-Javadoc)
3011    *
3012    * @see
3013    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3014    * .ActionEvent)
3015    */
3016   @Override
3017   public void hideAllSelection_actionPerformed(ActionEvent e)
3018   {
3019     SequenceGroup sg = viewport.getSelectionGroup();
3020     viewport.expandColSelection(sg, false);
3021     viewport.hideAllSelectedSeqs();
3022     viewport.hideSelectedColumns();
3023     alignPanel.paintAlignment(true);
3024   }
3025
3026   /*
3027    * (non-Javadoc)
3028    *
3029    * @see
3030    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3031    * ActionEvent)
3032    */
3033   @Override
3034   public void showAllhidden_actionPerformed(ActionEvent e)
3035   {
3036     viewport.showAllHiddenColumns();
3037     viewport.showAllHiddenSeqs();
3038     alignPanel.paintAlignment(true);
3039   }
3040
3041   @Override
3042   public void hideSelColumns_actionPerformed(ActionEvent e)
3043   {
3044     viewport.hideSelectedColumns();
3045     alignPanel.paintAlignment(true);
3046   }
3047
3048   @Override
3049   public void hiddenMarkers_actionPerformed(ActionEvent e)
3050   {
3051     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3052     repaint();
3053   }
3054
3055   /**
3056    * DOCUMENT ME!
3057    *
3058    * @param e
3059    *          DOCUMENT ME!
3060    */
3061   @Override
3062   protected void scaleAbove_actionPerformed(ActionEvent e)
3063   {
3064     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3065     alignPanel.paintAlignment(true);
3066   }
3067
3068   /**
3069    * DOCUMENT ME!
3070    *
3071    * @param e
3072    *          DOCUMENT ME!
3073    */
3074   @Override
3075   protected void scaleLeft_actionPerformed(ActionEvent e)
3076   {
3077     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3078     alignPanel.paintAlignment(true);
3079   }
3080
3081   /**
3082    * DOCUMENT ME!
3083    *
3084    * @param e
3085    *          DOCUMENT ME!
3086    */
3087   @Override
3088   protected void scaleRight_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setScaleRightWrapped(scaleRight.isSelected());
3091     alignPanel.paintAlignment(true);
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3104     alignPanel.paintAlignment(true);
3105   }
3106
3107   /**
3108    * DOCUMENT ME!
3109    *
3110    * @param e
3111    *          DOCUMENT ME!
3112    */
3113   @Override
3114   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setShowText(viewTextMenuItem.isSelected());
3117     alignPanel.paintAlignment(true);
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   public FeatureSettings featureSettings;
3134
3135   @Override
3136   public void featureSettings_actionPerformed(ActionEvent e)
3137   {
3138     if (featureSettings != null)
3139     {
3140       featureSettings.close();
3141       featureSettings = null;
3142     }
3143     if (!showSeqFeatures.isSelected())
3144     {
3145       // make sure features are actually displayed
3146       showSeqFeatures.setSelected(true);
3147       showSeqFeatures_actionPerformed(null);
3148     }
3149     featureSettings = new FeatureSettings(this);
3150   }
3151
3152   /**
3153    * Set or clear 'Show Sequence Features'
3154    *
3155    * @param evt
3156    *          DOCUMENT ME!
3157    */
3158   @Override
3159   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3160   {
3161     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3162     alignPanel.paintAlignment(true);
3163     if (alignPanel.getOverviewPanel() != null)
3164     {
3165       alignPanel.getOverviewPanel().updateOverviewImage();
3166     }
3167   }
3168
3169   /**
3170    * Set or clear 'Show Sequence Features'
3171    *
3172    * @param evt
3173    *          DOCUMENT ME!
3174    */
3175   @Override
3176   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3177   {
3178     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3179             .isSelected());
3180     if (viewport.isShowSequenceFeaturesHeight())
3181     {
3182       // ensure we're actually displaying features
3183       viewport.setShowSequenceFeatures(true);
3184       showSeqFeatures.setSelected(true);
3185     }
3186     alignPanel.paintAlignment(true);
3187     if (alignPanel.getOverviewPanel() != null)
3188     {
3189       alignPanel.getOverviewPanel().updateOverviewImage();
3190     }
3191   }
3192
3193   /**
3194    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3195    * the annotations panel as a whole.
3196    *
3197    * The options to show/hide all annotations should be enabled when the panel
3198    * is shown, and disabled when the panel is hidden.
3199    *
3200    * @param e
3201    */
3202   @Override
3203   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3204   {
3205     final boolean setVisible = annotationPanelMenuItem.isSelected();
3206     viewport.setShowAnnotation(setVisible);
3207     this.showAllSeqAnnotations.setEnabled(setVisible);
3208     this.hideAllSeqAnnotations.setEnabled(setVisible);
3209     this.showAllAlAnnotations.setEnabled(setVisible);
3210     this.hideAllAlAnnotations.setEnabled(setVisible);
3211     alignPanel.updateLayout();
3212   }
3213
3214   @Override
3215   public void alignmentProperties()
3216   {
3217     JEditorPane editPane = new JEditorPane("text/html", "");
3218     editPane.setEditable(false);
3219     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3220             .formatAsHtml();
3221     editPane.setText(MessageManager.formatMessage("label.html_content",
3222             new Object[]
3223             { contents.toString() }));
3224     JInternalFrame frame = new JInternalFrame();
3225     frame.getContentPane().add(new JScrollPane(editPane));
3226
3227     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3228             "label.alignment_properties", new Object[]
3229             { getTitle() }), 500, 400);
3230   }
3231
3232   /**
3233    * DOCUMENT ME!
3234    *
3235    * @param e
3236    *          DOCUMENT ME!
3237    */
3238   @Override
3239   public void overviewMenuItem_actionPerformed(ActionEvent e)
3240   {
3241     if (alignPanel.overviewPanel != null)
3242     {
3243       return;
3244     }
3245
3246     JInternalFrame frame = new JInternalFrame();
3247     OverviewPanel overview = new OverviewPanel(alignPanel);
3248     frame.setContentPane(overview);
3249     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3250             "label.overview_params", new Object[]
3251             { this.getTitle() }), frame.getWidth(), frame.getHeight());
3252     frame.pack();
3253     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3254     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3255     {
3256       @Override
3257       public void internalFrameClosed(
3258               javax.swing.event.InternalFrameEvent evt)
3259       {
3260         alignPanel.setOverviewPanel(null);
3261       };
3262     });
3263
3264     alignPanel.setOverviewPanel(overview);
3265   }
3266
3267   @Override
3268   public void textColour_actionPerformed(ActionEvent e)
3269   {
3270     new TextColourChooser().chooseColour(alignPanel, null);
3271   }
3272
3273   /**
3274    * DOCUMENT ME!
3275    *
3276    * @param e
3277    *          DOCUMENT ME!
3278    */
3279   @Override
3280   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3281   {
3282     changeColour(null);
3283   }
3284
3285   /**
3286    * DOCUMENT ME!
3287    *
3288    * @param e
3289    *          DOCUMENT ME!
3290    */
3291   @Override
3292   public void clustalColour_actionPerformed(ActionEvent e)
3293   {
3294     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3295             viewport.getHiddenRepSequences()));
3296   }
3297
3298   /**
3299    * DOCUMENT ME!
3300    *
3301    * @param e
3302    *          DOCUMENT ME!
3303    */
3304   @Override
3305   public void zappoColour_actionPerformed(ActionEvent e)
3306   {
3307     changeColour(new ZappoColourScheme());
3308   }
3309
3310   /**
3311    * DOCUMENT ME!
3312    *
3313    * @param e
3314    *          DOCUMENT ME!
3315    */
3316   @Override
3317   public void taylorColour_actionPerformed(ActionEvent e)
3318   {
3319     changeColour(new TaylorColourScheme());
3320   }
3321
3322   /**
3323    * DOCUMENT ME!
3324    *
3325    * @param e
3326    *          DOCUMENT ME!
3327    */
3328   @Override
3329   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3330   {
3331     changeColour(new HydrophobicColourScheme());
3332   }
3333
3334   /**
3335    * DOCUMENT ME!
3336    *
3337    * @param e
3338    *          DOCUMENT ME!
3339    */
3340   @Override
3341   public void helixColour_actionPerformed(ActionEvent e)
3342   {
3343     changeColour(new HelixColourScheme());
3344   }
3345
3346   /**
3347    * DOCUMENT ME!
3348    *
3349    * @param e
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void strandColour_actionPerformed(ActionEvent e)
3354   {
3355     changeColour(new StrandColourScheme());
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   public void turnColour_actionPerformed(ActionEvent e)
3366   {
3367     changeColour(new TurnColourScheme());
3368   }
3369
3370   /**
3371    * DOCUMENT ME!
3372    *
3373    * @param e
3374    *          DOCUMENT ME!
3375    */
3376   @Override
3377   public void buriedColour_actionPerformed(ActionEvent e)
3378   {
3379     changeColour(new BuriedColourScheme());
3380   }
3381
3382   /**
3383    * DOCUMENT ME!
3384    *
3385    * @param e
3386    *          DOCUMENT ME!
3387    */
3388   @Override
3389   public void nucleotideColour_actionPerformed(ActionEvent e)
3390   {
3391     changeColour(new NucleotideColourScheme());
3392   }
3393
3394   @Override
3395   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3396   {
3397     changeColour(new PurinePyrimidineColourScheme());
3398   }
3399
3400   /*
3401    * public void covariationColour_actionPerformed(ActionEvent e) {
3402    * changeColour(new
3403    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3404    * ()[0])); }
3405    */
3406   @Override
3407   public void annotationColour_actionPerformed(ActionEvent e)
3408   {
3409     new AnnotationColourChooser(viewport, alignPanel);
3410   }
3411
3412   @Override
3413   public void annotationColumn_actionPerformed(ActionEvent e)
3414   {
3415     new AnnotationColumnChooser(viewport, alignPanel);
3416   }
3417
3418   @Override
3419   public void rnahelicesColour_actionPerformed(ActionEvent e)
3420   {
3421     new RNAHelicesColourChooser(viewport, alignPanel);
3422   }
3423
3424   /**
3425    * DOCUMENT ME!
3426    *
3427    * @param e
3428    *          DOCUMENT ME!
3429    */
3430   @Override
3431   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3432   {
3433     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3434   }
3435
3436   /**
3437    * DOCUMENT ME!
3438    *
3439    * @param cs
3440    *          DOCUMENT ME!
3441    */
3442   public void changeColour(ColourSchemeI cs)
3443   {
3444     // TODO: compare with applet and pull up to model method
3445     int threshold = 0;
3446
3447     if (cs != null)
3448     {
3449       if (viewport.getAbovePIDThreshold())
3450       {
3451         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3452                 "Background");
3453         cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3454       }
3455       else
3456       {
3457         cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3458       }
3459
3460       if (viewport.getConservationSelected())
3461       {
3462
3463         Alignment al = (Alignment) viewport.getAlignment();
3464         Conservation c = new Conservation("All",
3465                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3466                 al.getWidth() - 1);
3467
3468         c.calculate();
3469         c.verdict(false, viewport.getConsPercGaps());
3470
3471         cs.setConservation(c);
3472
3473         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3474                 cs, "Background"));
3475       }
3476       else
3477       {
3478         cs.setConservation(null);
3479       }
3480
3481       cs.setConsensus(viewport.getSequenceConsensusHash());
3482     }
3483
3484     viewport.setGlobalColourScheme(cs);
3485
3486     if (viewport.getColourAppliesToAllGroups())
3487     {
3488
3489       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3490       {
3491         if (cs == null)
3492         {
3493           sg.cs = null;
3494           continue;
3495         }
3496
3497         if (cs instanceof ClustalxColourScheme)
3498         {
3499           sg.cs = new ClustalxColourScheme(sg,
3500                   viewport.getHiddenRepSequences());
3501         }
3502         else if (cs instanceof UserColourScheme)
3503         {
3504           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3505         }
3506         else
3507         {
3508           try
3509           {
3510             sg.cs = cs.getClass().newInstance();
3511           } catch (Exception ex)
3512           {
3513           }
3514         }
3515
3516         if (viewport.getAbovePIDThreshold()
3517                 || cs instanceof PIDColourScheme
3518                 || cs instanceof Blosum62ColourScheme)
3519         {
3520           sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3521
3522           sg.cs.setConsensus(AAFrequency.calculate(
3523                   sg.getSequences(viewport.getHiddenRepSequences()),
3524                   sg.getStartRes(), sg.getEndRes() + 1));
3525         }
3526         else
3527         {
3528           sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3529         }
3530
3531         if (viewport.getConservationSelected())
3532         {
3533           Conservation c = new Conservation("Group",
3534                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3535                           .getHiddenRepSequences()), sg.getStartRes(),
3536                   sg.getEndRes() + 1);
3537           c.calculate();
3538           c.verdict(false, viewport.getConsPercGaps());
3539           sg.cs.setConservation(c);
3540         }
3541         else
3542         {
3543           sg.cs.setConservation(null);
3544         }
3545       }
3546     }
3547
3548     if (alignPanel.getOverviewPanel() != null)
3549     {
3550       alignPanel.getOverviewPanel().updateOverviewImage();
3551     }
3552
3553     alignPanel.paintAlignment(true);
3554   }
3555
3556   /**
3557    * DOCUMENT ME!
3558    *
3559    * @param e
3560    *          DOCUMENT ME!
3561    */
3562   @Override
3563   protected void modifyPID_actionPerformed(ActionEvent e)
3564   {
3565     if (viewport.getAbovePIDThreshold()
3566             && viewport.getGlobalColourScheme() != null)
3567     {
3568       SliderPanel.setPIDSliderSource(alignPanel,
3569               viewport.getGlobalColourScheme(), "Background");
3570       SliderPanel.showPIDSlider();
3571     }
3572   }
3573
3574   /**
3575    * DOCUMENT ME!
3576    *
3577    * @param e
3578    *          DOCUMENT ME!
3579    */
3580   @Override
3581   protected void modifyConservation_actionPerformed(ActionEvent e)
3582   {
3583     if (viewport.getConservationSelected()
3584             && viewport.getGlobalColourScheme() != null)
3585     {
3586       SliderPanel.setConservationSlider(alignPanel,
3587               viewport.getGlobalColourScheme(), "Background");
3588       SliderPanel.showConservationSlider();
3589     }
3590   }
3591
3592   /**
3593    * DOCUMENT ME!
3594    *
3595    * @param e
3596    *          DOCUMENT ME!
3597    */
3598   @Override
3599   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3600   {
3601     viewport.setConservationSelected(conservationMenuItem.isSelected());
3602
3603     viewport.setAbovePIDThreshold(false);
3604     abovePIDThreshold.setSelected(false);
3605
3606     changeColour(viewport.getGlobalColourScheme());
3607
3608     modifyConservation_actionPerformed(null);
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param e
3615    *          DOCUMENT ME!
3616    */
3617   @Override
3618   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3619   {
3620     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3621
3622     conservationMenuItem.setSelected(false);
3623     viewport.setConservationSelected(false);
3624
3625     changeColour(viewport.getGlobalColourScheme());
3626
3627     modifyPID_actionPerformed(null);
3628   }
3629
3630   /**
3631    * DOCUMENT ME!
3632    *
3633    * @param e
3634    *          DOCUMENT ME!
3635    */
3636   @Override
3637   public void userDefinedColour_actionPerformed(ActionEvent e)
3638   {
3639     if (e.getActionCommand().equals(
3640             MessageManager.getString("action.user_defined")))
3641     {
3642       new UserDefinedColours(alignPanel, null);
3643     }
3644     else
3645     {
3646       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3647               .getUserColourSchemes().get(e.getActionCommand());
3648
3649       changeColour(udc);
3650     }
3651   }
3652
3653   public void updateUserColourMenu()
3654   {
3655
3656     Component[] menuItems = colourMenu.getMenuComponents();
3657     int iSize = menuItems.length;
3658     for (int i = 0; i < iSize; i++)
3659     {
3660       if (menuItems[i].getName() != null
3661               && menuItems[i].getName().equals("USER_DEFINED"))
3662       {
3663         colourMenu.remove(menuItems[i]);
3664         iSize--;
3665       }
3666     }
3667     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3668     {
3669       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3670               .getUserColourSchemes().keys();
3671
3672       while (userColours.hasMoreElements())
3673       {
3674         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3675                 userColours.nextElement().toString());
3676         radioItem.setName("USER_DEFINED");
3677         radioItem.addMouseListener(new MouseAdapter()
3678         {
3679           @Override
3680           public void mousePressed(MouseEvent evt)
3681           {
3682             if (evt.isControlDown()
3683                     || SwingUtilities.isRightMouseButton(evt))
3684             {
3685               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3686
3687               int option = JOptionPane.showInternalConfirmDialog(
3688                       jalview.gui.Desktop.desktop,
3689                       MessageManager
3690                               .getString("label.remove_from_default_list"),
3691                       MessageManager
3692                               .getString("label.remove_user_defined_colour"),
3693                       JOptionPane.YES_NO_OPTION);
3694               if (option == JOptionPane.YES_OPTION)
3695               {
3696                 jalview.gui.UserDefinedColours
3697                         .removeColourFromDefaults(radioItem.getText());
3698                 colourMenu.remove(radioItem);
3699               }
3700               else
3701               {
3702                 radioItem.addActionListener(new ActionListener()
3703                 {
3704                   @Override
3705                   public void actionPerformed(ActionEvent evt)
3706                   {
3707                     userDefinedColour_actionPerformed(evt);
3708                   }
3709                 });
3710               }
3711             }
3712           }
3713         });
3714         radioItem.addActionListener(new ActionListener()
3715         {
3716           @Override
3717           public void actionPerformed(ActionEvent evt)
3718           {
3719             userDefinedColour_actionPerformed(evt);
3720           }
3721         });
3722
3723         colourMenu.insert(radioItem, 15);
3724         colours.add(radioItem);
3725       }
3726     }
3727   }
3728
3729   /**
3730    * DOCUMENT ME!
3731    *
3732    * @param e
3733    *          DOCUMENT ME!
3734    */
3735   @Override
3736   public void PIDColour_actionPerformed(ActionEvent e)
3737   {
3738     changeColour(new PIDColourScheme());
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3749   {
3750     changeColour(new Blosum62ColourScheme());
3751   }
3752
3753   /**
3754    * DOCUMENT ME!
3755    *
3756    * @param e
3757    *          DOCUMENT ME!
3758    */
3759   @Override
3760   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3761   {
3762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3764             .getAlignment().getSequenceAt(0), null);
3765     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3766             viewport.getAlignment()));
3767     alignPanel.paintAlignment(true);
3768   }
3769
3770   /**
3771    * DOCUMENT ME!
3772    *
3773    * @param e
3774    *          DOCUMENT ME!
3775    */
3776   @Override
3777   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3778   {
3779     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3780     AlignmentSorter.sortByID(viewport.getAlignment());
3781     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3782             viewport.getAlignment()));
3783     alignPanel.paintAlignment(true);
3784   }
3785
3786   /**
3787    * DOCUMENT ME!
3788    *
3789    * @param e
3790    *          DOCUMENT ME!
3791    */
3792   @Override
3793   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3794   {
3795     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3796     AlignmentSorter.sortByLength(viewport.getAlignment());
3797     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3798             viewport.getAlignment()));
3799     alignPanel.paintAlignment(true);
3800   }
3801
3802   /**
3803    * DOCUMENT ME!
3804    *
3805    * @param e
3806    *          DOCUMENT ME!
3807    */
3808   @Override
3809   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3810   {
3811     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3812     AlignmentSorter.sortByGroup(viewport.getAlignment());
3813     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3814             viewport.getAlignment()));
3815
3816     alignPanel.paintAlignment(true);
3817   }
3818
3819   /**
3820    * DOCUMENT ME!
3821    *
3822    * @param e
3823    *          DOCUMENT ME!
3824    */
3825   @Override
3826   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3827   {
3828     new RedundancyPanel(alignPanel, this);
3829   }
3830
3831   /**
3832    * DOCUMENT ME!
3833    *
3834    * @param e
3835    *          DOCUMENT ME!
3836    */
3837   @Override
3838   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3839   {
3840     if ((viewport.getSelectionGroup() == null)
3841             || (viewport.getSelectionGroup().getSize() < 2))
3842     {
3843       JOptionPane.showInternalMessageDialog(this, MessageManager
3844               .getString("label.you_must_select_least_two_sequences"),
3845               MessageManager.getString("label.invalid_selection"),
3846               JOptionPane.WARNING_MESSAGE);
3847     }
3848     else
3849     {
3850       JInternalFrame frame = new JInternalFrame();
3851       frame.setContentPane(new PairwiseAlignPanel(viewport));
3852       Desktop.addInternalFrame(frame,
3853               MessageManager.getString("action.pairwise_alignment"), 600,
3854               500);
3855     }
3856   }
3857
3858   /**
3859    * DOCUMENT ME!
3860    *
3861    * @param e
3862    *          DOCUMENT ME!
3863    */
3864   @Override
3865   public void PCAMenuItem_actionPerformed(ActionEvent e)
3866   {
3867     if (((viewport.getSelectionGroup() != null)
3868             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3869             .getSelectionGroup().getSize() > 0))
3870             || (viewport.getAlignment().getHeight() < 4))
3871     {
3872       JOptionPane
3873               .showInternalMessageDialog(
3874                       this,
3875                       MessageManager
3876                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3877                       MessageManager
3878                               .getString("label.sequence_selection_insufficient"),
3879                       JOptionPane.WARNING_MESSAGE);
3880
3881       return;
3882     }
3883
3884     new PCAPanel(alignPanel);
3885   }
3886
3887   @Override
3888   public void autoCalculate_actionPerformed(ActionEvent e)
3889   {
3890     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3891     if (viewport.autoCalculateConsensus)
3892     {
3893       viewport.firePropertyChange("alignment", null, viewport
3894               .getAlignment().getSequences());
3895     }
3896   }
3897
3898   @Override
3899   public void sortByTreeOption_actionPerformed(ActionEvent e)
3900   {
3901     viewport.sortByTree = sortByTree.isSelected();
3902   }
3903
3904   @Override
3905   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3906   {
3907     viewport.followSelection = listenToViewSelections.isSelected();
3908   }
3909
3910   /**
3911    * DOCUMENT ME!
3912    *
3913    * @param e
3914    *          DOCUMENT ME!
3915    */
3916   @Override
3917   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3918   {
3919     newTreePanel("AV", "PID", "Average distance tree using PID");
3920   }
3921
3922   /**
3923    * DOCUMENT ME!
3924    *
3925    * @param e
3926    *          DOCUMENT ME!
3927    */
3928   @Override
3929   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3930   {
3931     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3932   }
3933
3934   /**
3935    * DOCUMENT ME!
3936    *
3937    * @param e
3938    *          DOCUMENT ME!
3939    */
3940   @Override
3941   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3942   {
3943     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3944   }
3945
3946   /**
3947    * DOCUMENT ME!
3948    *
3949    * @param e
3950    *          DOCUMENT ME!
3951    */
3952   @Override
3953   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3954   {
3955     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3956   }
3957
3958   /**
3959    * DOCUMENT ME!
3960    *
3961    * @param type
3962    *          DOCUMENT ME!
3963    * @param pwType
3964    *          DOCUMENT ME!
3965    * @param title
3966    *          DOCUMENT ME!
3967    */
3968   void newTreePanel(String type, String pwType, String title)
3969   {
3970     TreePanel tp;
3971
3972     if (viewport.getSelectionGroup() != null
3973             && viewport.getSelectionGroup().getSize() > 0)
3974     {
3975       if (viewport.getSelectionGroup().getSize() < 3)
3976       {
3977         JOptionPane
3978                 .showMessageDialog(
3979                         Desktop.desktop,
3980                         MessageManager
3981                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3982                         MessageManager
3983                                 .getString("label.not_enough_sequences"),
3984                         JOptionPane.WARNING_MESSAGE);
3985         return;
3986       }
3987
3988       SequenceGroup sg = viewport.getSelectionGroup();
3989
3990       /* Decide if the selection is a column region */
3991       for (SequenceI _s : sg.getSequences())
3992       {
3993         if (_s.getLength() < sg.getEndRes())
3994         {
3995           JOptionPane
3996                   .showMessageDialog(
3997                           Desktop.desktop,
3998                           MessageManager
3999                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4000                           MessageManager
4001                                   .getString("label.sequences_selection_not_aligned"),
4002                           JOptionPane.WARNING_MESSAGE);
4003
4004           return;
4005         }
4006       }
4007
4008       title = title + " on region";
4009       tp = new TreePanel(alignPanel, type, pwType);
4010     }
4011     else
4012     {
4013       // are the visible sequences aligned?
4014       if (!viewport.getAlignment().isAligned(false))
4015       {
4016         JOptionPane
4017                 .showMessageDialog(
4018                         Desktop.desktop,
4019                         MessageManager
4020                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4021                         MessageManager
4022                                 .getString("label.sequences_not_aligned"),
4023                         JOptionPane.WARNING_MESSAGE);
4024
4025         return;
4026       }
4027
4028       if (viewport.getAlignment().getHeight() < 2)
4029       {
4030         return;
4031       }
4032
4033       tp = new TreePanel(alignPanel, type, pwType);
4034     }
4035
4036     title += " from ";
4037
4038     if (viewport.viewName != null)
4039     {
4040       title += viewport.viewName + " of ";
4041     }
4042
4043     title += this.title;
4044
4045     Desktop.addInternalFrame(tp, title, 600, 500);
4046   }
4047
4048   /**
4049    * DOCUMENT ME!
4050    *
4051    * @param title
4052    *          DOCUMENT ME!
4053    * @param order
4054    *          DOCUMENT ME!
4055    */
4056   public void addSortByOrderMenuItem(String title,
4057           final AlignmentOrder order)
4058   {
4059     final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4060     sort.add(item);
4061     item.addActionListener(new java.awt.event.ActionListener()
4062     {
4063       @Override
4064       public void actionPerformed(ActionEvent e)
4065       {
4066         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4067
4068         // TODO: JBPNote - have to map order entries to curent SequenceI
4069         // pointers
4070         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4071
4072         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4073                 .getAlignment()));
4074
4075         alignPanel.paintAlignment(true);
4076       }
4077     });
4078   }
4079
4080   /**
4081    * Add a new sort by annotation score menu item
4082    *
4083    * @param sort
4084    *          the menu to add the option to
4085    * @param scoreLabel
4086    *          the label used to retrieve scores for each sequence on the
4087    *          alignment
4088    */
4089   public void addSortByAnnotScoreMenuItem(JMenu sort,
4090           final String scoreLabel)
4091   {
4092     final JMenuItem item = new JMenuItem(scoreLabel);
4093     sort.add(item);
4094     item.addActionListener(new java.awt.event.ActionListener()
4095     {
4096       @Override
4097       public void actionPerformed(ActionEvent e)
4098       {
4099         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4100         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4101                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4102         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4103                 viewport.getAlignment()));
4104         alignPanel.paintAlignment(true);
4105       }
4106     });
4107   }
4108
4109   /**
4110    * last hash for alignment's annotation array - used to minimise cost of
4111    * rebuild.
4112    */
4113   protected int _annotationScoreVectorHash;
4114
4115   /**
4116    * search the alignment and rebuild the sort by annotation score submenu the
4117    * last alignment annotation vector hash is stored to minimize cost of
4118    * rebuilding in subsequence calls.
4119    *
4120    */
4121   @Override
4122   public void buildSortByAnnotationScoresMenu()
4123   {
4124     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4125     {
4126       return;
4127     }
4128
4129     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4130     {
4131       sortByAnnotScore.removeAll();
4132       // almost certainly a quicker way to do this - but we keep it simple
4133       Hashtable scoreSorts = new Hashtable();
4134       AlignmentAnnotation aann[];
4135       for (SequenceI sqa : viewport.getAlignment().getSequences())
4136       {
4137         aann = sqa.getAnnotation();
4138         for (int i = 0; aann != null && i < aann.length; i++)
4139         {
4140           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4141           {
4142             scoreSorts.put(aann[i].label, aann[i].label);
4143           }
4144         }
4145       }
4146       Enumeration labels = scoreSorts.keys();
4147       while (labels.hasMoreElements())
4148       {
4149         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4150                 (String) labels.nextElement());
4151       }
4152       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4153       scoreSorts.clear();
4154
4155       _annotationScoreVectorHash = viewport.getAlignment()
4156               .getAlignmentAnnotation().hashCode();
4157     }
4158   }
4159
4160   /**
4161    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4162    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4163    * call. Listeners are added to remove the menu item when the treePanel is
4164    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4165    * modified.
4166    *
4167    * @param treePanel
4168    *          Displayed tree window.
4169    * @param title
4170    *          SortBy menu item title.
4171    */
4172   @Override
4173   public void buildTreeMenu()
4174   {
4175     calculateTree.removeAll();
4176     // build the calculate menu
4177
4178     for (final String type : new String[]
4179     { "NJ", "AV" })
4180     {
4181       String treecalcnm = MessageManager.getString("label.tree_calc_"
4182               + type.toLowerCase());
4183       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4184       {
4185         JMenuItem tm = new JMenuItem();
4186         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4187         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4188         {
4189           String smn = MessageManager.getStringOrReturn(
4190                   "label.score_model_", sm.getName());
4191           final String title = MessageManager.formatMessage(
4192                   "label.treecalc_title", treecalcnm, smn);
4193           tm.setText(title);//
4194           tm.addActionListener(new java.awt.event.ActionListener()
4195           {
4196             @Override
4197             public void actionPerformed(ActionEvent e)
4198             {
4199               newTreePanel(type, pwtype, title);
4200             }
4201           });
4202           calculateTree.add(tm);
4203         }
4204
4205       }
4206     }
4207     sortByTreeMenu.removeAll();
4208
4209     List<Component> comps = PaintRefresher.components.get(viewport
4210             .getSequenceSetId());
4211     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4212     for (Component comp : comps)
4213     {
4214       if (comp instanceof TreePanel)
4215       {
4216         treePanels.add((TreePanel) comp);
4217       }
4218     }
4219
4220     if (treePanels.size() < 1)
4221     {
4222       sortByTreeMenu.setVisible(false);
4223       return;
4224     }
4225
4226     sortByTreeMenu.setVisible(true);
4227
4228     for (final TreePanel tp : treePanels)
4229     {
4230       final JMenuItem item = new JMenuItem(tp.getTitle());
4231       item.addActionListener(new java.awt.event.ActionListener()
4232       {
4233         @Override
4234         public void actionPerformed(ActionEvent e)
4235         {
4236           tp.sortByTree_actionPerformed();
4237           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4238
4239         }
4240       });
4241
4242       sortByTreeMenu.add(item);
4243     }
4244   }
4245
4246   public boolean sortBy(AlignmentOrder alorder, String undoname)
4247   {
4248     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4249     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4250     if (undoname != null)
4251     {
4252       addHistoryItem(new OrderCommand(undoname, oldOrder,
4253               viewport.getAlignment()));
4254     }
4255     alignPanel.paintAlignment(true);
4256     return true;
4257   }
4258
4259   /**
4260    * Work out whether the whole set of sequences or just the selected set will
4261    * be submitted for multiple alignment.
4262    *
4263    */
4264   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4265   {
4266     // Now, check we have enough sequences
4267     AlignmentView msa = null;
4268
4269     if ((viewport.getSelectionGroup() != null)
4270             && (viewport.getSelectionGroup().getSize() > 1))
4271     {
4272       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4273       // some common interface!
4274       /*
4275        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4276        * SequenceI[sz = seqs.getSize(false)];
4277        *
4278        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4279        * seqs.getSequenceAt(i); }
4280        */
4281       msa = viewport.getAlignmentView(true);
4282     }
4283     else if (viewport.getSelectionGroup() != null
4284             && viewport.getSelectionGroup().getSize() == 1)
4285     {
4286       int option = JOptionPane.showConfirmDialog(this,
4287               MessageManager.getString("warn.oneseq_msainput_selection"),
4288               MessageManager.getString("label.invalid_selection"),
4289               JOptionPane.OK_CANCEL_OPTION);
4290       if (option == JOptionPane.OK_OPTION)
4291       {
4292         msa = viewport.getAlignmentView(false);
4293       }
4294     }
4295     else
4296     {
4297       msa = viewport.getAlignmentView(false);
4298     }
4299     return msa;
4300   }
4301
4302   /**
4303    * Decides what is submitted to a secondary structure prediction service: the
4304    * first sequence in the alignment, or in the current selection, or, if the
4305    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4306    * region or the whole alignment. (where the first sequence in the set is the
4307    * one that the prediction will be for).
4308    */
4309   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4310   {
4311     AlignmentView seqs = null;
4312
4313     if ((viewport.getSelectionGroup() != null)
4314             && (viewport.getSelectionGroup().getSize() > 0))
4315     {
4316       seqs = viewport.getAlignmentView(true);
4317     }
4318     else
4319     {
4320       seqs = viewport.getAlignmentView(false);
4321     }
4322     // limit sequences - JBPNote in future - could spawn multiple prediction
4323     // jobs
4324     // TODO: viewport.getAlignment().isAligned is a global state - the local
4325     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4326     if (!viewport.getAlignment().isAligned(false))
4327     {
4328       seqs.setSequences(new SeqCigar[]
4329       { seqs.getSequences()[0] });
4330       // TODO: if seqs.getSequences().length>1 then should really have warned
4331       // user!
4332
4333     }
4334     return seqs;
4335   }
4336
4337   /**
4338    * DOCUMENT ME!
4339    *
4340    * @param e
4341    *          DOCUMENT ME!
4342    */
4343   @Override
4344   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4345   {
4346     // Pick the tree file
4347     JalviewFileChooser chooser = new JalviewFileChooser(
4348             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4349     chooser.setFileView(new JalviewFileView());
4350     chooser.setDialogTitle(MessageManager
4351             .getString("label.select_newick_like_tree_file"));
4352     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4353
4354     int value = chooser.showOpenDialog(null);
4355
4356     if (value == JalviewFileChooser.APPROVE_OPTION)
4357     {
4358       String choice = chooser.getSelectedFile().getPath();
4359       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4360       jalview.io.NewickFile fin = null;
4361       try
4362       {
4363         fin = new jalview.io.NewickFile(choice, "File");
4364         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4365       } catch (Exception ex)
4366       {
4367         JOptionPane
4368                 .showMessageDialog(
4369                         Desktop.desktop,
4370                         ex.getMessage(),
4371                         MessageManager
4372                                 .getString("label.problem_reading_tree_file"),
4373                         JOptionPane.WARNING_MESSAGE);
4374         ex.printStackTrace();
4375       }
4376       if (fin != null && fin.hasWarningMessage())
4377       {
4378         JOptionPane.showMessageDialog(Desktop.desktop, fin
4379                 .getWarningMessage(), MessageManager
4380                 .getString("label.possible_problem_with_tree_file"),
4381                 JOptionPane.WARNING_MESSAGE);
4382       }
4383     }
4384   }
4385
4386   @Override
4387   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4388   {
4389     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4390   }
4391
4392   public TreePanel ShowNewickTree(NewickFile nf, String title)
4393   {
4394     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4395   }
4396
4397   public TreePanel ShowNewickTree(NewickFile nf, String title,
4398           AlignmentView input)
4399   {
4400     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4401   }
4402
4403   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4404           int h, int x, int y)
4405   {
4406     return ShowNewickTree(nf, title, null, w, h, x, y);
4407   }
4408
4409   /**
4410    * Add a treeviewer for the tree extracted from a newick file object to the
4411    * current alignment view
4412    *
4413    * @param nf
4414    *          the tree
4415    * @param title
4416    *          tree viewer title
4417    * @param input
4418    *          Associated alignment input data (or null)
4419    * @param w
4420    *          width
4421    * @param h
4422    *          height
4423    * @param x
4424    *          position
4425    * @param y
4426    *          position
4427    * @return TreePanel handle
4428    */
4429   public TreePanel ShowNewickTree(NewickFile nf, String title,
4430           AlignmentView input, int w, int h, int x, int y)
4431   {
4432     TreePanel tp = null;
4433
4434     try
4435     {
4436       nf.parse();
4437
4438       if (nf.getTree() != null)
4439       {
4440         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4441
4442         tp.setSize(w, h);
4443
4444         if (x > 0 && y > 0)
4445         {
4446           tp.setLocation(x, y);
4447         }
4448
4449         Desktop.addInternalFrame(tp, title, w, h);
4450       }
4451     } catch (Exception ex)
4452     {
4453       ex.printStackTrace();
4454     }
4455
4456     return tp;
4457   }
4458
4459   private boolean buildingMenu = false;
4460
4461   /**
4462    * Generates menu items and listener event actions for web service clients
4463    *
4464    */
4465   public void BuildWebServiceMenu()
4466   {
4467     while (buildingMenu)
4468     {
4469       try
4470       {
4471         System.err.println("Waiting for building menu to finish.");
4472         Thread.sleep(10);
4473       } catch (Exception e)
4474       {
4475       }
4476     }
4477     final AlignFrame me = this;
4478     buildingMenu = true;
4479     new Thread(new Runnable()
4480     {
4481       @Override
4482       public void run()
4483       {
4484         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4485         try
4486         {
4487           System.err.println("Building ws menu again "
4488                   + Thread.currentThread());
4489           // TODO: add support for context dependent disabling of services based
4490           // on
4491           // alignment and current selection
4492           // TODO: add additional serviceHandle parameter to specify abstract
4493           // handler
4494           // class independently of AbstractName
4495           // TODO: add in rediscovery GUI function to restart discoverer
4496           // TODO: group services by location as well as function and/or
4497           // introduce
4498           // object broker mechanism.
4499           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4500           final IProgressIndicator af = me;
4501           final JMenu msawsmenu = new JMenu("Alignment");
4502           final JMenu secstrmenu = new JMenu(
4503                   "Secondary Structure Prediction");
4504           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4505           final JMenu analymenu = new JMenu("Analysis");
4506           final JMenu dismenu = new JMenu("Protein Disorder");
4507           // final JMenu msawsmenu = new
4508           // JMenu(MessageManager.getString("label.alignment"));
4509           // final JMenu secstrmenu = new
4510           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4511           // final JMenu seqsrchmenu = new
4512           // JMenu(MessageManager.getString("label.sequence_database_search"));
4513           // final JMenu analymenu = new
4514           // JMenu(MessageManager.getString("label.analysis"));
4515           // final JMenu dismenu = new
4516           // JMenu(MessageManager.getString("label.protein_disorder"));
4517           // JAL-940 - only show secondary structure prediction services from
4518           // the legacy server
4519           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4520               // &&
4521           Discoverer.services != null && (Discoverer.services.size() > 0))
4522           {
4523             // TODO: refactor to allow list of AbstractName/Handler bindings to
4524             // be
4525             // stored or retrieved from elsewhere
4526             // No MSAWS used any more:
4527             // Vector msaws = null; // (Vector)
4528             // Discoverer.services.get("MsaWS");
4529             Vector secstrpr = (Vector) Discoverer.services
4530                     .get("SecStrPred");
4531             if (secstrpr != null)
4532             {
4533               // Add any secondary structure prediction services
4534               for (int i = 0, j = secstrpr.size(); i < j; i++)
4535               {
4536                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4537                         .get(i);
4538                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4539                         .getServiceClient(sh);
4540                 int p = secstrmenu.getItemCount();
4541                 impl.attachWSMenuEntry(secstrmenu, me);
4542                 int q = secstrmenu.getItemCount();
4543                 for (int litm = p; litm < q; litm++)
4544                 {
4545                   legacyItems.add(secstrmenu.getItem(litm));
4546                 }
4547               }
4548             }
4549           }
4550
4551           // Add all submenus in the order they should appear on the web
4552           // services menu
4553           wsmenu.add(msawsmenu);
4554           wsmenu.add(secstrmenu);
4555           wsmenu.add(dismenu);
4556           wsmenu.add(analymenu);
4557           // No search services yet
4558           // wsmenu.add(seqsrchmenu);
4559
4560           javax.swing.SwingUtilities.invokeLater(new Runnable()
4561           {
4562             @Override
4563             public void run()
4564             {
4565               try
4566               {
4567                 webService.removeAll();
4568                 // first, add discovered services onto the webservices menu
4569                 if (wsmenu.size() > 0)
4570                 {
4571                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4572                   {
4573                     webService.add(wsmenu.get(i));
4574                   }
4575                 }
4576                 else
4577                 {
4578                   webService.add(me.webServiceNoServices);
4579                 }
4580                 // TODO: move into separate menu builder class.
4581                 boolean new_sspred = false;
4582                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4583                 {
4584                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4585                   if (jws2servs != null)
4586                   {
4587                     if (jws2servs.hasServices())
4588                     {
4589                       jws2servs.attachWSMenuEntry(webService, me);
4590                       for (Jws2Instance sv : jws2servs.getServices())
4591                       {
4592                         if (sv.description.toLowerCase().contains("jpred"))
4593                         {
4594                           for (JMenuItem jmi : legacyItems)
4595                           {
4596                             jmi.setVisible(false);
4597                           }
4598                         }
4599                       }
4600
4601                     }
4602                     if (jws2servs.isRunning())
4603                     {
4604                       JMenuItem tm = new JMenuItem(
4605                               "Still discovering JABA Services");
4606                       tm.setEnabled(false);
4607                       webService.add(tm);
4608                     }
4609                   }
4610                 }
4611                 build_urlServiceMenu(me.webService);
4612                 build_fetchdbmenu(webService);
4613                 for (JMenu item : wsmenu)
4614                 {
4615                   if (item.getItemCount() == 0)
4616                   {
4617                     item.setEnabled(false);
4618                   }
4619                   else
4620                   {
4621                     item.setEnabled(true);
4622                   }
4623                 }
4624               } catch (Exception e)
4625               {
4626                 Cache.log
4627                         .debug("Exception during web service menu building process.",
4628                                 e);
4629               }
4630             }
4631           });
4632         } catch (Exception e)
4633         {
4634         }
4635         buildingMenu = false;
4636       }
4637     }).start();
4638
4639   }
4640
4641   /**
4642    * construct any groupURL type service menu entries.
4643    *
4644    * @param webService
4645    */
4646   private void build_urlServiceMenu(JMenu webService)
4647   {
4648     // TODO: remove this code when 2.7 is released
4649     // DEBUG - alignmentView
4650     /*
4651      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4652      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4653      *
4654      * @Override public void actionPerformed(ActionEvent e) {
4655      * jalview.datamodel.AlignmentView
4656      * .testSelectionViews(af.viewport.getAlignment(),
4657      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4658      *
4659      * }); webService.add(testAlView);
4660      */
4661     // TODO: refactor to RestClient discoverer and merge menu entries for
4662     // rest-style services with other types of analysis/calculation service
4663     // SHmmr test client - still being implemented.
4664     // DEBUG - alignmentView
4665
4666     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4667             .getRestClients())
4668     {
4669       client.attachWSMenuEntry(
4670               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4671               this);
4672     }
4673   }
4674
4675   /*
4676    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4677    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4678    * getProperty("LAST_DIRECTORY"));
4679    *
4680    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4681    * to Vamsas file"); chooser.setToolTipText("Export");
4682    *
4683    * int value = chooser.showSaveDialog(this);
4684    *
4685    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4686    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4687    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4688    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4689    */
4690   /**
4691    * prototype of an automatically enabled/disabled analysis function
4692    *
4693    */
4694   protected void setShowProductsEnabled()
4695   {
4696     SequenceI[] selection = viewport.getSequenceSelection();
4697     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4698             viewport.getAlignment().getDataset()))
4699     {
4700       showProducts.setEnabled(true);
4701
4702     }
4703     else
4704     {
4705       showProducts.setEnabled(false);
4706     }
4707   }
4708
4709   /**
4710    * search selection for sequence xRef products and build the show products
4711    * menu.
4712    *
4713    * @param selection
4714    * @param dataset
4715    * @return true if showProducts menu should be enabled.
4716    */
4717   public boolean canShowProducts(SequenceI[] selection,
4718           boolean isRegionSelection, Alignment dataset)
4719   {
4720     boolean showp = false;
4721     try
4722     {
4723       showProducts.removeAll();
4724       final boolean dna = viewport.getAlignment().isNucleotide();
4725       final Alignment ds = dataset;
4726       String[] ptypes = (selection == null || selection.length == 0) ? null
4727               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4728       // Object[] prods =
4729       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4730       // selection, dataset, true);
4731       final SequenceI[] sel = selection;
4732       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4733       {
4734         showp = true;
4735         final boolean isRegSel = isRegionSelection;
4736         final AlignFrame af = this;
4737         final String source = ptypes[t];
4738         JMenuItem xtype = new JMenuItem(ptypes[t]);
4739         xtype.addActionListener(new ActionListener()
4740         {
4741
4742           @Override
4743           public void actionPerformed(ActionEvent e)
4744           {
4745             // TODO: new thread for this call with vis-delay
4746             af.showProductsFor(af.viewport.getSequenceSelection(),
4747                     isRegSel, dna, source);
4748           }
4749
4750         });
4751         showProducts.add(xtype);
4752       }
4753       showProducts.setVisible(showp);
4754       showProducts.setEnabled(showp);
4755     } catch (Exception e)
4756     {
4757       jalview.bin.Cache.log
4758               .warn("canTranslate threw an exception - please report to help@jalview.org",
4759                       e);
4760       return false;
4761     }
4762     return showp;
4763   }
4764
4765   protected void showProductsFor(final SequenceI[] sel,
4766           final boolean isRegSel, final boolean dna, final String source)
4767   {
4768     Runnable foo = new Runnable()
4769     {
4770
4771       @Override
4772       public void run()
4773       {
4774         final long sttime = System.currentTimeMillis();
4775         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4776                 "status.searching_for_sequences_from", new Object[]
4777                 { source }), sttime);
4778         try
4779         {
4780           // update our local dataset reference
4781           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4782                   .getDataset();
4783           Alignment prods = CrossRef
4784                   .findXrefSequences(sel, dna, source, ds);
4785           if (prods != null)
4786           {
4787             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4788             for (int s = 0; s < sprods.length; s++)
4789             {
4790               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4791               if (ds.getSequences() == null
4792                       || !ds.getSequences().contains(
4793                               sprods[s].getDatasetSequence()))
4794               {
4795                 ds.addSequence(sprods[s].getDatasetSequence());
4796               }
4797               sprods[s].updatePDBIds();
4798             }
4799             Alignment al = new Alignment(sprods);
4800             al.setDataset(ds);
4801
4802             /*
4803              * Copy dna-to-protein mappings to new alignment
4804              */
4805             // TODO 1: no mappings are set up for EMBL product
4806             // TODO 2: if they were, should add them to protein alignment, not
4807             // dna
4808             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4809             for (AlignedCodonFrame acf : cf)
4810             {
4811               al.addCodonFrame(acf);
4812             }
4813             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4814                     DEFAULT_HEIGHT);
4815             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4816                     + " for " + ((isRegSel) ? "selected region of " : "")
4817                     + getTitle();
4818             naf.setTitle(newtitle);
4819
4820             // temporary flag until SplitFrame is released
4821             boolean asSplitFrame = Cache.getDefault(
4822                     Preferences.ENABLE_SPLIT_FRAME, false);
4823             if (asSplitFrame)
4824             {
4825               /*
4826                * Make a copy of this alignment (sharing the same dataset
4827                * sequences). If we are DNA, drop introns and update mappings
4828                */
4829               AlignmentI copyAlignment = null;
4830               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4831                       .getSequenceSelection();
4832               if (dna)
4833               {
4834                 copyAlignment = AlignmentUtils.makeExonAlignment(
4835                         sequenceSelection, cf);
4836                 al.getCodonFrames().clear();
4837                 al.getCodonFrames().addAll(cf);
4838                 final StructureSelectionManager ssm = StructureSelectionManager
4839                         .getStructureSelectionManager(Desktop.instance);
4840                 ssm.addMappings(cf);
4841               }
4842               else
4843               {
4844                 copyAlignment = new Alignment(new Alignment(
4845                         sequenceSelection));
4846               }
4847               AlignFrame copyThis = new AlignFrame(copyAlignment,
4848                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4849               copyThis.setTitle(AlignFrame.this.getTitle());
4850               // SplitFrame with dna above, protein below
4851               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4852                       dna ? naf : copyThis);
4853               naf.setVisible(true);
4854               copyThis.setVisible(true);
4855               String linkedTitle = MessageManager
4856                       .getString("label.linked_view_title");
4857               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4858             }
4859             else
4860             {
4861               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4862                       DEFAULT_HEIGHT);
4863             }
4864           }
4865           else
4866           {
4867             System.err.println("No Sequences generated for xRef type "
4868                     + source);
4869           }
4870         } catch (Exception e)
4871         {
4872           jalview.bin.Cache.log.error(
4873                   "Exception when finding crossreferences", e);
4874         } catch (OutOfMemoryError e)
4875         {
4876           new OOMWarning("whilst fetching crossreferences", e);
4877         } catch (Error e)
4878         {
4879           jalview.bin.Cache.log.error("Error when finding crossreferences",
4880                   e);
4881         }
4882         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4883                 "status.finished_searching_for_sequences_from",
4884                 new Object[]
4885                 { source }),
4886                 sttime);
4887       }
4888
4889     };
4890     Thread frunner = new Thread(foo);
4891     frunner.start();
4892   }
4893
4894   public boolean canShowTranslationProducts(SequenceI[] selection,
4895           AlignmentI alignment)
4896   {
4897     // old way
4898     try
4899     {
4900       return (jalview.analysis.Dna.canTranslate(selection,
4901               viewport.getViewAsVisibleContigs(true)));
4902     } catch (Exception e)
4903     {
4904       jalview.bin.Cache.log
4905               .warn("canTranslate threw an exception - please report to help@jalview.org",
4906                       e);
4907       return false;
4908     }
4909   }
4910
4911   /**
4912    * Construct and display a new frame containing the translation of this
4913    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4914    */
4915   @Override
4916   public void showTranslation_actionPerformed(ActionEvent e)
4917   {
4918     AlignmentI al = null;
4919     try
4920     {
4921       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4922
4923       al = dna.translateCdna();
4924     } catch (Exception ex)
4925     {
4926       jalview.bin.Cache.log.error(
4927               "Exception during translation. Please report this !", ex);
4928       final String msg = MessageManager
4929               .getString("label.error_when_translating_sequences_submit_bug_report");
4930       final String title = MessageManager
4931               .getString("label.implementation_error")
4932               + MessageManager.getString("translation_failed");
4933       JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4934               JOptionPane.ERROR_MESSAGE);
4935       return;
4936     }
4937     if (al == null || al.getHeight() == 0)
4938     {
4939       final String msg = MessageManager
4940               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4941       final String title = MessageManager
4942               .getString("label.translation_failed");
4943       JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4944               JOptionPane.WARNING_MESSAGE);
4945     }
4946     else
4947     {
4948       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4949       af.setFileFormat(this.currentFileFormat);
4950       final String newTitle = MessageManager.formatMessage(
4951               "label.translation_of_params", new Object[]
4952               { this.getTitle() });
4953       af.setTitle(newTitle);
4954       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
4955       {
4956         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4957         viewport.openSplitFrame(af, new Alignment(seqs),
4958                 al.getCodonFrames());
4959       }
4960       else
4961       {
4962         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4963                 DEFAULT_HEIGHT);
4964       }
4965     }
4966   }
4967
4968   /**
4969    * Set the file format
4970    *
4971    * @param fileFormat
4972    */
4973   public void setFileFormat(String fileFormat)
4974   {
4975     this.currentFileFormat = fileFormat;
4976   }
4977
4978   /**
4979    * Try to load a features file onto the alignment.
4980    *
4981    * @param file
4982    *          contents or path to retrieve file
4983    * @param type
4984    *          access mode of file (see jalview.io.AlignFile)
4985    * @return true if features file was parsed corectly.
4986    */
4987   public boolean parseFeaturesFile(String file, String type)
4988   {
4989     boolean featuresFile = false;
4990     try
4991     {
4992       featuresFile = new FeaturesFile(file, type).parse(viewport
4993               .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
4994               .getFeatureRenderer().getFeatureColours(), false,
4995               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4996     } catch (Exception ex)
4997     {
4998       ex.printStackTrace();
4999     }
5000
5001     if (featuresFile)
5002     {
5003       viewport.setShowSequenceFeatures(true);
5004       showSeqFeatures.setSelected(true);
5005       if (alignPanel.getSeqPanel().seqCanvas.fr != null)
5006       {
5007         // update the min/max ranges where necessary
5008         alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
5009       }
5010       if (featureSettings != null)
5011       {
5012         featureSettings.setTableData();
5013       }
5014       alignPanel.paintAlignment(true);
5015     }
5016
5017     return featuresFile;
5018   }
5019
5020   @Override
5021   public void dragEnter(DropTargetDragEvent evt)
5022   {
5023   }
5024
5025   @Override
5026   public void dragExit(DropTargetEvent evt)
5027   {
5028   }
5029
5030   @Override
5031   public void dragOver(DropTargetDragEvent evt)
5032   {
5033   }
5034
5035   @Override
5036   public void dropActionChanged(DropTargetDragEvent evt)
5037   {
5038   }
5039
5040   @Override
5041   public void drop(DropTargetDropEvent evt)
5042   {
5043     Transferable t = evt.getTransferable();
5044     java.util.List files = null;
5045
5046     try
5047     {
5048       DataFlavor uriListFlavor = new DataFlavor(
5049               "text/uri-list;class=java.lang.String");
5050       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5051       {
5052         // Works on Windows and MacOSX
5053         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5054         files = (java.util.List) t
5055                 .getTransferData(DataFlavor.javaFileListFlavor);
5056       }
5057       else if (t.isDataFlavorSupported(uriListFlavor))
5058       {
5059         // This is used by Unix drag system
5060         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5061         String data = (String) t.getTransferData(uriListFlavor);
5062         files = new java.util.ArrayList(1);
5063         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5064                 data, "\r\n"); st.hasMoreTokens();)
5065         {
5066           String s = st.nextToken();
5067           if (s.startsWith("#"))
5068           {
5069             // the line is a comment (as per the RFC 2483)
5070             continue;
5071           }
5072
5073           java.net.URI uri = new java.net.URI(s);
5074           // check to see if we can handle this kind of URI
5075           if (uri.getScheme().toLowerCase().startsWith("http"))
5076           {
5077             files.add(uri.toString());
5078           }
5079           else
5080           {
5081             // otherwise preserve old behaviour: catch all for file objects
5082             java.io.File file = new java.io.File(uri);
5083             files.add(file.toString());
5084           }
5085         }
5086       }
5087     } catch (Exception e)
5088     {
5089       e.printStackTrace();
5090     }
5091     if (files != null)
5092     {
5093       try
5094       {
5095         // check to see if any of these files have names matching sequences in
5096         // the alignment
5097         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5098                 .getAlignment().getSequencesArray());
5099         /**
5100          * Object[] { String,SequenceI}
5101          */
5102         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5103         ArrayList<String> filesnotmatched = new ArrayList<String>();
5104         for (int i = 0; i < files.size(); i++)
5105         {
5106           String file = files.get(i).toString();
5107           String pdbfn = "";
5108           String protocol = FormatAdapter.checkProtocol(file);
5109           if (protocol == jalview.io.FormatAdapter.FILE)
5110           {
5111             File fl = new File(file);
5112             pdbfn = fl.getName();
5113           }
5114           else if (protocol == jalview.io.FormatAdapter.URL)
5115           {
5116             URL url = new URL(file);
5117             pdbfn = url.getFile();
5118           }
5119           if (pdbfn.length() > 0)
5120           {
5121             // attempt to find a match in the alignment
5122             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5123             int l = 0, c = pdbfn.indexOf(".");
5124             while (mtch == null && c != -1)
5125             {
5126               do
5127               {
5128                 l = c;
5129               } while ((c = pdbfn.indexOf(".", l)) > l);
5130               if (l > -1)
5131               {
5132                 pdbfn = pdbfn.substring(0, l);
5133               }
5134               mtch = idm.findAllIdMatches(pdbfn);
5135             }
5136             if (mtch != null)
5137             {
5138               String type = null;
5139               try
5140               {
5141                 type = new IdentifyFile().Identify(file, protocol);
5142               } catch (Exception ex)
5143               {
5144                 type = null;
5145               }
5146               if (type != null)
5147               {
5148                 if (type.equalsIgnoreCase("PDB"))
5149                 {
5150                   filesmatched.add(new Object[]
5151                   { file, protocol, mtch });
5152                   continue;
5153                 }
5154               }
5155             }
5156             // File wasn't named like one of the sequences or wasn't a PDB file.
5157             filesnotmatched.add(file);
5158           }
5159         }
5160         int assocfiles = 0;
5161         if (filesmatched.size() > 0)
5162         {
5163           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5164                   || JOptionPane
5165                           .showConfirmDialog(
5166                                   this,
5167                                   MessageManager
5168                                           .formatMessage(
5169                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5170                                                   new Object[]
5171                                                   { Integer.valueOf(
5172                                                           filesmatched
5173                                                                   .size())
5174                                                           .toString() }),
5175                                   MessageManager
5176                                           .getString("label.automatically_associate_pdb_files_by_name"),
5177                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5178
5179           {
5180             for (Object[] fm : filesmatched)
5181             {
5182               // try and associate
5183               // TODO: may want to set a standard ID naming formalism for
5184               // associating PDB files which have no IDs.
5185               for (SequenceI toassoc : (SequenceI[]) fm[2])
5186               {
5187                 PDBEntry pe = new AssociatePdbFileWithSeq()
5188                         .associatePdbWithSeq((String) fm[0],
5189                                 (String) fm[1], toassoc, false,
5190                                 Desktop.instance);
5191                 if (pe != null)
5192                 {
5193                   System.err.println("Associated file : "
5194                           + ((String) fm[0]) + " with "
5195                           + toassoc.getDisplayId(true));
5196                   assocfiles++;
5197                 }
5198               }
5199               alignPanel.paintAlignment(true);
5200             }
5201           }
5202         }
5203         if (filesnotmatched.size() > 0)
5204         {
5205           if (assocfiles > 0
5206                   && (Cache.getDefault(
5207                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5208                           .showConfirmDialog(
5209                                   this,
5210                                   "<html>"+MessageManager
5211                                           .formatMessage(
5212                                                   "label.ignore_unmatched_dropped_files_info",
5213                                                   new Object[]
5214                                                   { Integer.valueOf(
5215                                                           filesnotmatched
5216                                                                   .size())
5217                                                           .toString() })+"</html>",
5218                                   MessageManager
5219                                           .getString("label.ignore_unmatched_dropped_files"),
5220                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5221           {
5222             return;
5223           }
5224           for (String fn : filesnotmatched)
5225           {
5226             loadJalviewDataFile(fn, null, null, null);
5227           }
5228
5229         }
5230       } catch (Exception ex)
5231       {
5232         ex.printStackTrace();
5233       }
5234     }
5235   }
5236
5237   /**
5238    * Attempt to load a "dropped" file or URL string: First by testing whether
5239    * it's and Annotation file, then a JNet file, and finally a features file. If
5240    * all are false then the user may have dropped an alignment file onto this
5241    * AlignFrame.
5242    *
5243    * @param file
5244    *          either a filename or a URL string.
5245    */
5246   public void loadJalviewDataFile(String file, String protocol,
5247           String format, SequenceI assocSeq)
5248   {
5249     try
5250     {
5251       if (protocol == null)
5252       {
5253         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5254       }
5255       // if the file isn't identified, or not positively identified as some
5256       // other filetype (PFAM is default unidentified alignment file type) then
5257       // try to parse as annotation.
5258       boolean isAnnotation = (format == null || format
5259               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5260               .annotateAlignmentView(viewport, file, protocol)
5261               : false;
5262
5263       if (!isAnnotation)
5264       {
5265         // first see if its a T-COFFEE score file
5266         TCoffeeScoreFile tcf = null;
5267         try
5268         {
5269           tcf = new TCoffeeScoreFile(file, protocol);
5270           if (tcf.isValid())
5271           {
5272             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5273             {
5274               tcoffeeColour.setEnabled(true);
5275               tcoffeeColour.setSelected(true);
5276               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5277               isAnnotation = true;
5278               statusBar
5279                       .setText(MessageManager
5280                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5281             }
5282             else
5283             {
5284               // some problem - if no warning its probable that the ID matching
5285               // process didn't work
5286               JOptionPane
5287                       .showMessageDialog(
5288                               Desktop.desktop,
5289                               tcf.getWarningMessage() == null ? MessageManager
5290                                       .getString("label.check_file_matches_sequence_ids_alignment")
5291                                       : tcf.getWarningMessage(),
5292                               MessageManager
5293                                       .getString("label.problem_reading_tcoffee_score_file"),
5294                               JOptionPane.WARNING_MESSAGE);
5295             }
5296           }
5297           else
5298           {
5299             tcf = null;
5300           }
5301         } catch (Exception x)
5302         {
5303           Cache.log
5304                   .debug("Exception when processing data source as T-COFFEE score file",
5305                           x);
5306           tcf = null;
5307         }
5308         if (tcf == null)
5309         {
5310           // try to see if its a JNet 'concise' style annotation file *before*
5311           // we
5312           // try to parse it as a features file
5313           if (format == null)
5314           {
5315             format = new IdentifyFile().Identify(file, protocol);
5316           }
5317           if (format.equalsIgnoreCase("JnetFile"))
5318           {
5319             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5320                     file, protocol);
5321             new JnetAnnotationMaker();
5322             JnetAnnotationMaker.add_annotation(predictions,
5323                     viewport.getAlignment(), 0, false);
5324             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5325             viewport.getAlignment().setSeqrep(repseq);
5326             ColumnSelection cs = new ColumnSelection();
5327             cs.hideInsertionsFor(repseq);
5328             viewport.setColumnSelection(cs);
5329             isAnnotation = true;
5330           }
5331           else
5332           {
5333             /*
5334              * if (format.equalsIgnoreCase("PDB")) {
5335              *
5336              * String pdbfn = ""; // try to match up filename with sequence id
5337              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5338              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5339              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5340              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5341              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5342              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5343              * // attempt to find a match in the alignment SequenceI mtch =
5344              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5345              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5346              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5347              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5348              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5349              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5350              * { System.err.println("Associated file : " + file + " with " +
5351              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5352              * TODO: maybe need to load as normal otherwise return; } }
5353              */
5354             // try to parse it as a features file
5355             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5356             // if it wasn't a features file then we just treat it as a general
5357             // alignment file to load into the current view.
5358             if (!isGroupsFile)
5359             {
5360               new FileLoader().LoadFile(viewport, file, protocol, format);
5361             }
5362             else
5363             {
5364               alignPanel.paintAlignment(true);
5365             }
5366           }
5367         }
5368       }
5369       if (isAnnotation)
5370       {
5371
5372         alignPanel.adjustAnnotationHeight();
5373         viewport.updateSequenceIdColours();
5374         buildSortByAnnotationScoresMenu();
5375         alignPanel.paintAlignment(true);
5376       }
5377     } catch (Exception ex)
5378     {
5379       ex.printStackTrace();
5380     } catch (OutOfMemoryError oom)
5381     {
5382       try
5383       {
5384         System.gc();
5385       } catch (Exception x)
5386       {
5387       }
5388       ;
5389       new OOMWarning(
5390               "loading data "
5391                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5392                               : "using " + protocol + " from " + file)
5393                               : ".")
5394                       + (format != null ? "(parsing as '" + format
5395                               + "' file)" : ""), oom, Desktop.desktop);
5396     }
5397   }
5398
5399   /**
5400    * Method invoked by the ChangeListener on the tabbed pane, in other words
5401    * when a different tabbed pane is selected by the user or programmatically.
5402    */
5403   @Override
5404   public void tabSelectionChanged(int index)
5405   {
5406     if (index > -1)
5407     {
5408       alignPanel = alignPanels.get(index);
5409       viewport = alignPanel.av;
5410       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5411       setMenusFromViewport(viewport);
5412     }
5413
5414     /*
5415      * If there is a frame linked to this one in a SplitPane, switch it to the
5416      * same view tab index. No infinite recursion of calls should happen, since
5417      * tabSelectionChanged() should not get invoked on setting the selected
5418      * index to an unchanged value. Guard against setting an invalid index
5419      * before the new view peer tab has been created.
5420      */
5421     final AlignViewportI peer = viewport.getCodingComplement();
5422     if (peer != null)
5423     {
5424       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5425       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5426       {
5427         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5428       }
5429     }
5430   }
5431
5432   /**
5433    * On right mouse click on view tab, prompt for and set new view name.
5434    */
5435   @Override
5436   public void tabbedPane_mousePressed(MouseEvent e)
5437   {
5438     if (SwingUtilities.isRightMouseButton(e))
5439     {
5440       String msg = MessageManager.getString("label.enter_view_name");
5441       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5442               JOptionPane.QUESTION_MESSAGE);
5443
5444       if (reply != null)
5445       {
5446         viewport.viewName = reply;
5447         // TODO warn if reply is in getExistingViewNames()?
5448         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5449       }
5450     }
5451   }
5452
5453   public AlignViewport getCurrentView()
5454   {
5455     return viewport;
5456   }
5457
5458   /**
5459    * Open the dialog for regex description parsing.
5460    */
5461   @Override
5462   protected void extractScores_actionPerformed(ActionEvent e)
5463   {
5464     ParseProperties pp = new jalview.analysis.ParseProperties(
5465             viewport.getAlignment());
5466     // TODO: verify regex and introduce GUI dialog for version 2.5
5467     // if (pp.getScoresFromDescription("col", "score column ",
5468     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5469     // true)>0)
5470     if (pp.getScoresFromDescription("description column",
5471             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5472     {
5473       buildSortByAnnotationScoresMenu();
5474     }
5475   }
5476
5477   /*
5478    * (non-Javadoc)
5479    *
5480    * @see
5481    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5482    * )
5483    */
5484   @Override
5485   protected void showDbRefs_actionPerformed(ActionEvent e)
5486   {
5487     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5488   }
5489
5490   /*
5491    * (non-Javadoc)
5492    *
5493    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5494    * ActionEvent)
5495    */
5496   @Override
5497   protected void showNpFeats_actionPerformed(ActionEvent e)
5498   {
5499     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5500   }
5501
5502   /**
5503    * find the viewport amongst the tabs in this alignment frame and close that
5504    * tab
5505    *
5506    * @param av
5507    */
5508   public boolean closeView(AlignViewportI av)
5509   {
5510     if (viewport == av)
5511     {
5512       this.closeMenuItem_actionPerformed(false);
5513       return true;
5514     }
5515     Component[] comp = tabbedPane.getComponents();
5516     for (int i = 0; comp != null && i < comp.length; i++)
5517     {
5518       if (comp[i] instanceof AlignmentPanel)
5519       {
5520         if (((AlignmentPanel) comp[i]).av == av)
5521         {
5522           // close the view.
5523           closeView((AlignmentPanel) comp[i]);
5524           return true;
5525         }
5526       }
5527     }
5528     return false;
5529   }
5530
5531   protected void build_fetchdbmenu(JMenu webService)
5532   {
5533     // Temporary hack - DBRef Fetcher always top level ws entry.
5534     // TODO We probably want to store a sequence database checklist in
5535     // preferences and have checkboxes.. rather than individual sources selected
5536     // here
5537     final JMenu rfetch = new JMenu(
5538             MessageManager.getString("action.fetch_db_references"));
5539     rfetch.setToolTipText(MessageManager
5540             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5541     webService.add(rfetch);
5542
5543     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5544             MessageManager.getString("option.trim_retrieved_seqs"));
5545     trimrs.setToolTipText(MessageManager
5546             .getString("label.trim_retrieved_sequences"));
5547     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5548     trimrs.addActionListener(new ActionListener()
5549     {
5550       @Override
5551       public void actionPerformed(ActionEvent e)
5552       {
5553         trimrs.setSelected(trimrs.isSelected());
5554         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5555                 Boolean.valueOf(trimrs.isSelected()).toString());
5556       };
5557     });
5558     rfetch.add(trimrs);
5559     JMenuItem fetchr = new JMenuItem(
5560             MessageManager.getString("label.standard_databases"));
5561     fetchr.setToolTipText(MessageManager
5562             .getString("label.fetch_embl_uniprot"));
5563     fetchr.addActionListener(new ActionListener()
5564     {
5565
5566       @Override
5567       public void actionPerformed(ActionEvent e)
5568       {
5569         new Thread(new Runnable()
5570         {
5571
5572           @Override
5573           public void run()
5574           {
5575             new jalview.ws.DBRefFetcher(alignPanel.av
5576                     .getSequenceSelection(), alignPanel.alignFrame)
5577                     .fetchDBRefs(false);
5578           }
5579         }).start();
5580
5581       }
5582
5583     });
5584     rfetch.add(fetchr);
5585     final AlignFrame me = this;
5586     new Thread(new Runnable()
5587     {
5588       @Override
5589       public void run()
5590       {
5591         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5592                 .getSequenceFetcherSingleton(me);
5593         javax.swing.SwingUtilities.invokeLater(new Runnable()
5594         {
5595           @Override
5596           public void run()
5597           {
5598             String[] dbclasses = sf.getOrderedSupportedSources();
5599             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5600             // jalview.util.QuickSort.sort(otherdb, otherdb);
5601             List<DbSourceProxy> otherdb;
5602             JMenu dfetch = new JMenu();
5603             JMenu ifetch = new JMenu();
5604             JMenuItem fetchr = null;
5605             int comp = 0, icomp = 0, mcomp = 15;
5606             String mname = null;
5607             int dbi = 0;
5608             for (String dbclass : dbclasses)
5609             {
5610               otherdb = sf.getSourceProxy(dbclass);
5611               // add a single entry for this class, or submenu allowing 'fetch
5612               // all' or pick one
5613               if (otherdb == null || otherdb.size() < 1)
5614               {
5615                 continue;
5616               }
5617               // List<DbSourceProxy> dbs=otherdb;
5618               // otherdb=new ArrayList<DbSourceProxy>();
5619               // for (DbSourceProxy db:dbs)
5620               // {
5621               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5622               // }
5623               if (mname == null)
5624               {
5625                 mname = "From " + dbclass;
5626               }
5627               if (otherdb.size() == 1)
5628               {
5629                 final DbSourceProxy[] dassource = otherdb
5630                         .toArray(new DbSourceProxy[0]);
5631                 DbSourceProxy src = otherdb.get(0);
5632                 fetchr = new JMenuItem(src.getDbSource());
5633                 fetchr.addActionListener(new ActionListener()
5634                 {
5635
5636                   @Override
5637                   public void actionPerformed(ActionEvent e)
5638                   {
5639                     new Thread(new Runnable()
5640                     {
5641
5642                       @Override
5643                       public void run()
5644                       {
5645                         new jalview.ws.DBRefFetcher(alignPanel.av
5646                                 .getSequenceSelection(),
5647                                 alignPanel.alignFrame, dassource)
5648                                 .fetchDBRefs(false);
5649                       }
5650                     }).start();
5651                   }
5652
5653                 });
5654                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5655                 dfetch.add(fetchr);
5656                 comp++;
5657               }
5658               else
5659               {
5660                 final DbSourceProxy[] dassource = otherdb
5661                         .toArray(new DbSourceProxy[0]);
5662                 // fetch all entry
5663                 DbSourceProxy src = otherdb.get(0);
5664                 fetchr = new JMenuItem(MessageManager.formatMessage(
5665                         "label.fetch_all_param", new Object[]
5666                         { src.getDbSource() }));
5667                 fetchr.addActionListener(new ActionListener()
5668                 {
5669                   @Override
5670                   public void actionPerformed(ActionEvent e)
5671                   {
5672                     new Thread(new Runnable()
5673                     {
5674
5675                       @Override
5676                       public void run()
5677                       {
5678                         new jalview.ws.DBRefFetcher(alignPanel.av
5679                                 .getSequenceSelection(),
5680                                 alignPanel.alignFrame, dassource)
5681                                 .fetchDBRefs(false);
5682                       }
5683                     }).start();
5684                   }
5685                 });
5686
5687                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5688                 dfetch.add(fetchr);
5689                 comp++;
5690                 // and then build the rest of the individual menus
5691                 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5692                 icomp = 0;
5693                 String imname = null;
5694                 int i = 0;
5695                 for (DbSourceProxy sproxy : otherdb)
5696                 {
5697                   String dbname = sproxy.getDbName();
5698                   String sname = dbname.length() > 5 ? dbname.substring(0,
5699                           5) + "..." : dbname;
5700                   String msname = dbname.length() > 10 ? dbname.substring(
5701                           0, 10) + "..." : dbname;
5702                   if (imname == null)
5703                   {
5704                     imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5705                   }
5706                   fetchr = new JMenuItem(msname);
5707                   final DbSourceProxy[] dassrc =
5708                   { sproxy };
5709                   fetchr.addActionListener(new ActionListener()
5710                   {
5711
5712                     @Override
5713                     public void actionPerformed(ActionEvent e)
5714                     {
5715                       new Thread(new Runnable()
5716                       {
5717
5718                         @Override
5719                         public void run()
5720                         {
5721                           new jalview.ws.DBRefFetcher(alignPanel.av
5722                                   .getSequenceSelection(),
5723                                   alignPanel.alignFrame, dassrc)
5724                                   .fetchDBRefs(false);
5725                         }
5726                       }).start();
5727                     }
5728
5729                   });
5730                   fetchr.setToolTipText("<html>"
5731                           + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5732                   ifetch.add(fetchr);
5733                   ++i;
5734                   if (++icomp >= mcomp || i == (otherdb.size()))
5735                   {
5736                     ifetch.setText(MessageManager.formatMessage(
5737                             "label.source_to_target", imname, sname));
5738                     dfetch.add(ifetch);
5739                     ifetch = new JMenu();
5740                     imname = null;
5741                     icomp = 0;
5742                     comp++;
5743                   }
5744                 }
5745               }
5746               ++dbi;
5747               if (comp >= mcomp || dbi >= (dbclasses.length))
5748               {
5749                 dfetch.setText(MessageManager.formatMessage(
5750                         "label.source_to_target", mname, dbclass));
5751                 rfetch.add(dfetch);
5752                 dfetch = new JMenu();
5753                 mname = null;
5754                 comp = 0;
5755               }
5756             }
5757           }
5758         });
5759       }
5760     }).start();
5761
5762   }
5763
5764   /**
5765    * Left justify the whole alignment.
5766    */
5767   @Override
5768   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5769   {
5770     AlignmentI al = viewport.getAlignment();
5771     al.justify(false);
5772     viewport.firePropertyChange("alignment", null, al);
5773   }
5774
5775   /**
5776    * Right justify the whole alignment.
5777    */
5778   @Override
5779   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5780   {
5781     AlignmentI al = viewport.getAlignment();
5782     al.justify(true);
5783     viewport.firePropertyChange("alignment", null, al);
5784   }
5785
5786   public void setShowSeqFeatures(boolean b)
5787   {
5788     showSeqFeatures.setSelected(b);
5789     viewport.setShowSequenceFeatures(b);
5790   }
5791
5792   /*
5793    * (non-Javadoc)
5794    *
5795    * @see
5796    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5797    * awt.event.ActionEvent)
5798    */
5799   @Override
5800   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5801   {
5802     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5803     alignPanel.paintAlignment(true);
5804   }
5805
5806   /*
5807    * (non-Javadoc)
5808    *
5809    * @see
5810    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5811    * .ActionEvent)
5812    */
5813   @Override
5814   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5815   {
5816     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5817     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5818
5819   }
5820
5821   /*
5822    * (non-Javadoc)
5823    *
5824    * @see
5825    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5826    * .event.ActionEvent)
5827    */
5828   @Override
5829   protected void showGroupConservation_actionPerformed(ActionEvent e)
5830   {
5831     viewport.setShowGroupConservation(showGroupConservation.getState());
5832     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5833   }
5834
5835   /*
5836    * (non-Javadoc)
5837    *
5838    * @see
5839    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5840    * .event.ActionEvent)
5841    */
5842   @Override
5843   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5844   {
5845     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5846     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5847   }
5848
5849   /*
5850    * (non-Javadoc)
5851    *
5852    * @see
5853    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5854    * .event.ActionEvent)
5855    */
5856   @Override
5857   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5858   {
5859     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5860     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5861   }
5862
5863   @Override
5864   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5865   {
5866     showSequenceLogo.setState(true);
5867     viewport.setShowSequenceLogo(true);
5868     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5869     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5870   }
5871
5872   @Override
5873   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5874   {
5875     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5876   }
5877
5878   /*
5879    * (non-Javadoc)
5880    *
5881    * @see
5882    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5883    * .event.ActionEvent)
5884    */
5885   @Override
5886   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5887   {
5888     if (avc.makeGroupsFromSelection())
5889     {
5890       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5891       alignPanel.updateAnnotation();
5892       alignPanel.paintAlignment(true);
5893     }
5894   }
5895   public void clearAlignmentSeqRep()
5896   {
5897     // TODO refactor alignmentseqrep to controller
5898     if (viewport.getAlignment().hasSeqrep()) {
5899       viewport.getAlignment().setSeqrep(null);
5900       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5901       alignPanel.updateAnnotation();
5902       alignPanel.paintAlignment(true);
5903     }
5904   }
5905
5906   @Override
5907   protected void createGroup_actionPerformed(ActionEvent e)
5908   {
5909     if (avc.createGroup())
5910     {
5911       alignPanel.alignmentChanged();
5912     }
5913   }
5914
5915   @Override
5916   protected void unGroup_actionPerformed(ActionEvent e)
5917   {
5918     if (avc.unGroup())
5919     {
5920       alignPanel.alignmentChanged();
5921     }
5922   }
5923
5924   /**
5925    * make the given alignmentPanel the currently selected tab
5926    *
5927    * @param alignmentPanel
5928    */
5929   public void setDisplayedView(AlignmentPanel alignmentPanel)
5930   {
5931     if (!viewport.getSequenceSetId().equals(
5932             alignmentPanel.av.getSequenceSetId()))
5933     {
5934       throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5935     }
5936     if (tabbedPane != null
5937             && tabbedPane.getTabCount() > 0
5938             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5939                     .getSelectedIndex())
5940     {
5941       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5942     }
5943   }
5944
5945   /**
5946    * Action on selection of menu options to Show or Hide annotations.
5947    *
5948    * @param visible
5949    * @param forSequences
5950    *          update sequence-related annotations
5951    * @param forAlignment
5952    *          update non-sequence-related annotations
5953    */
5954   @Override
5955   protected void setAnnotationsVisibility(boolean visible,
5956           boolean forSequences, boolean forAlignment)
5957   {
5958     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5959             .getAlignmentAnnotation())
5960     {
5961       /*
5962        * don't display non-positional annotations on an alignment
5963        */
5964       if (aa.annotations == null)
5965       {
5966         continue;
5967       }
5968       boolean apply = (aa.sequenceRef == null && forAlignment)
5969               || (aa.sequenceRef != null && forSequences);
5970       if (apply)
5971       {
5972         aa.visible = visible;
5973       }
5974     }
5975     alignPanel.validateAnnotationDimensions(false);
5976     alignPanel.alignmentChanged();
5977   }
5978
5979   /**
5980    * Store selected annotation sort order for the view and repaint.
5981    */
5982   @Override
5983   protected void sortAnnotations_actionPerformed()
5984   {
5985     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5986     this.alignPanel.av
5987             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5988     alignPanel.paintAlignment(true);
5989   }
5990
5991   /**
5992    *
5993    * @return alignment panels in this alignment frame
5994    */
5995   public List<? extends AlignmentViewPanel> getAlignPanels()
5996   {
5997     return alignPanels == null ? Arrays.asList(alignPanel)
5998             : alignPanels;
5999   }
6000
6001   /**
6002    * Open a new alignment window, with the cDNA associated with this (protein)
6003    * alignment, aligned as is the protein.
6004    */
6005   protected void viewAsCdna_actionPerformed()
6006   {
6007     // TODO no longer a menu action - refactor as required
6008     final AlignmentI alignment = getViewport().getAlignment();
6009     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6010     if (mappings == null)
6011     {
6012       return;
6013     }
6014     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6015     for (SequenceI aaSeq : alignment.getSequences()) {
6016       for (AlignedCodonFrame acf : mappings) {
6017         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6018         if (dnaSeq != null)
6019         {
6020           /*
6021            * There is a cDNA mapping for this protein sequence - add to new
6022            * alignment. It will share the same dataset sequence as other mapped
6023            * cDNA (no new mappings need to be created).
6024            */
6025           final Sequence newSeq = new Sequence(dnaSeq);
6026           newSeq.setDatasetSequence(dnaSeq);
6027           cdnaSeqs.add(newSeq);
6028         }
6029       }
6030     }
6031     if (cdnaSeqs.size() == 0)
6032     {
6033       // show a warning dialog no mapped cDNA
6034       return;
6035     }
6036     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6037             .size()]));
6038     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6039             AlignFrame.DEFAULT_HEIGHT);
6040     cdna.alignAs(alignment);
6041     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6042             + this.title;
6043     Desktop.addInternalFrame(alignFrame, newtitle,
6044             AlignFrame.DEFAULT_WIDTH,
6045             AlignFrame.DEFAULT_HEIGHT);
6046   }
6047
6048   /**
6049    * Set visibility of dna/protein complement view (available when shown in a
6050    * split frame).
6051    *
6052    * @param show
6053    */
6054   @Override
6055   protected void showComplement_actionPerformed(boolean show)
6056   {
6057     SplitContainerI sf = getSplitViewContainer();
6058     if (sf != null) {
6059       sf.setComplementVisible(this, show);
6060     }
6061   }
6062
6063   public class ExportData
6064   {
6065     private AlignmentI alignment;
6066
6067     private String[] omitHidden;
6068
6069     private int[] startEnd;
6070
6071     public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
6072     {
6073       this.alignment = align;
6074       this.omitHidden = ommit;
6075       this.startEnd = startEnd;
6076     }
6077
6078     public AlignmentI getAlignment()
6079     {
6080       return alignment;
6081     }
6082
6083     public void setAlignment(AlignmentI alignment)
6084     {
6085       this.alignment = alignment;
6086     }
6087
6088     public String[] getOmitHidden()
6089     {
6090       return omitHidden;
6091     }
6092
6093     public void setOmitHidden(String[] omitHidden)
6094     {
6095       this.omitHidden = omitHidden;
6096     }
6097
6098     public int[] getStartEndPostions()
6099     {
6100       return startEnd;
6101     }
6102
6103     public void setStartEndPostions(int[] startEnd)
6104     {
6105       this.startEnd = startEnd;
6106     }
6107   }
6108
6109   @Override
6110   public void hideColumns(List<int[]> colsToHide)
6111   {
6112     for (int[] colRange : colsToHide)
6113     {
6114       viewport.hideColumns(colRange[0], colRange[1]);
6115     }
6116
6117   }
6118
6119   @Override
6120   public void syncHiddenSequences()
6121   {
6122     AlignmentI al = viewport.getAlignment();
6123     HiddenSequences hiddenSeqs = al.getHiddenSequences();
6124     for (SequenceI seq : al.getSequencesArray())
6125       {
6126         if (seq.isHidden())
6127         {
6128         hiddenSeqs.hideSequence(seq);
6129         }
6130       }
6131   }
6132 }
6133
6134 class PrintThread extends Thread
6135 {
6136   AlignmentPanel ap;
6137
6138   public PrintThread(AlignmentPanel ap)
6139   {
6140     this.ap = ap;
6141   }
6142
6143   static PageFormat pf;
6144
6145   @Override
6146   public void run()
6147   {
6148     PrinterJob printJob = PrinterJob.getPrinterJob();
6149
6150     if (pf != null)
6151     {
6152       printJob.setPrintable(ap, pf);
6153     }
6154     else
6155     {
6156       printJob.setPrintable(ap);
6157     }
6158
6159     if (printJob.printDialog())
6160     {
6161       try
6162       {
6163         printJob.print();
6164       } catch (Exception PrintException)
6165       {
6166         PrintException.printStackTrace();
6167       }
6168     }
6169   }
6170 }