src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.schemes.*;
  28
  29 public class GAlignFrame
  30     extends JInternalFrame
  31 {
  32   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  33   protected JMenu fileMenu = new JMenu();
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35   protected JMenu editMenu = new JMenu();
  36   protected JMenu viewMenu = new JMenu();
  37   protected JMenu colourMenu = new JMenu();
  38   protected JMenu calculateMenu = new JMenu();
  39   protected JMenu webService = new JMenu();
  40   protected JMenuItem webServiceNoServices;
  41   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  42   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  43   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  44   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  45   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  46   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  47   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  48   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  49   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  50   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  51   protected JMenuItem sortIDMenuItem = new JMenuItem();
  52   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  53   protected JMenu sortByAnnotScore = new JMenu();
  54   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  55   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  56   protected JMenuItem PCAMenuItem = new JMenuItem();
  57   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  58   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  59   BorderLayout borderLayout1 = new BorderLayout();
  60   public JLabel statusBar = new JLabel();
  61   protected JMenuItem saveAs = new JMenuItem();
  62   protected JMenu outputTextboxMenu = new JMenu();
  63   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  64   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  65   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  66   protected JRadioButtonMenuItem hydrophobicityColour = new
  67       JRadioButtonMenuItem();
  68   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  69   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  70   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  71   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  72   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  73   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  74   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  75   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  76   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  77   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  78   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  79   JMenuItem htmlMenuItem = new JMenuItem();
  80   JMenuItem overviewMenuItem = new JMenuItem();
  81   protected JMenuItem undoMenuItem = new JMenuItem();
  82   protected JMenuItem redoMenuItem = new JMenuItem();
  83   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  84   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  85   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  86   JMenuItem printMenuItem = new JMenuItem();
  87   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  88   JMenuItem findMenuItem = new JMenuItem();
  89   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  90   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
  91   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  92   JMenuItem deleteGroups = new JMenuItem();
  93   JMenuItem delete = new JMenuItem();
  94   JMenuItem copy = new JMenuItem();
  95   JMenuItem cut = new JMenuItem();
  96   JMenu pasteMenu = new JMenu();
  97   JMenuItem pasteNew = new JMenuItem();
  98   JMenuItem pasteThis = new JMenuItem();
  99   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 100   JMenuItem createPNG = new JMenuItem();
 101   protected JMenuItem font = new JMenuItem();
 102   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 103   JMenuItem epsFile = new JMenuItem();
 104   JMenuItem LoadtreeMenuItem = new JMenuItem();
 105   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 106   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 107   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 108   protected JMenuItem modifyPID = new JMenuItem();
 109   protected JMenuItem modifyConservation = new JMenuItem();
 110   protected JMenu sortByTreeMenu = new JMenu();
 111   protected JMenu sort = new JMenu();
 112   JMenu calculate = new JMenu();
 113   JMenu jMenu2 = new JMenu();
 114   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 115   protected ButtonGroup colours = new ButtonGroup();
 116   JMenuItem vamsasStore = new JMenuItem();
 117   protected JMenuItem showTranslation = new JMenuItem();
 118   protected JMenuItem extractScores = new JMenuItem();
 119   protected JMenu showProducts = new JMenu();
 120   public JMenuItem featureSettings = new JMenuItem();
 121   JMenuItem fetchSequence = new JMenuItem();
 122   JMenuItem annotationColour = new JMenuItem();
 123   JMenuItem associatedData = new JMenuItem();
 124   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 125   JMenu addSequenceMenu = new JMenu();
 126   JMenuItem addFromFile = new JMenuItem();
 127   JMenuItem addFromText = new JMenuItem();
 128   JMenuItem addFromURL = new JMenuItem();
 129   JMenuItem exportAnnotations = new JMenuItem();
 130   JMenuItem exportFeatures = new JMenuItem();
 131   protected JPanel statusPanel = new JPanel();
 132   GridLayout gridLayout1 = new GridLayout();
 133   JMenu jMenu3 = new JMenu();
 134   JMenuItem showAllSeqs = new JMenuItem();
 135   JMenuItem showAllColumns = new JMenuItem();
 136   JMenu hideMenu = new JMenu();
 137   JMenuItem hideSelSequences = new JMenuItem();
 138   JMenuItem hideSelColumns = new JMenuItem();
 139   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 140   JMenuItem invertColSel = new JMenuItem();
 141   protected JTabbedPane tabbedPane = new JTabbedPane();
 142   JMenuItem save = new JMenuItem();
 143   protected JMenuItem reload = new JMenuItem();
 144   JMenuItem newView = new JMenuItem();
 145   JMenuItem textColour = new JMenuItem();
 146   JMenu formatMenu = new JMenu();
 147   JMenu selectMenu = new JMenu();
 148   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 149   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 150   protected JMenuItem gatherViews = new JMenuItem();
 151   protected JMenuItem expandViews = new JMenuItem();
 152   JMenuItem pageSetup = new JMenuItem();
 153   JMenuItem alignmentProperties = new JMenuItem();
 154   public GAlignFrame()
 155   {
 156     try
 157     {
 158       jbInit();
 159       setJMenuBar(alignFrameMenuBar);
 160
 161       // dynamically fill save as menu with available formats
 162       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 163       {
 164         JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
 165                                        WRITEABLE_FORMATS[i]);
 166
 167         item.addActionListener(new java.awt.event.ActionListener()
 168         {
 169           public void actionPerformed(ActionEvent e)
 170           {
 171             outputText_actionPerformed(e);
 172           }
 173         });
 174
 175         outputTextboxMenu.add(item);
 176       }
 177     }
 178     catch (Exception e)
 179     {
 180     }
 181
 182     if (!new jalview.util.Platform().isAMac())
 183     {
 184       closeMenuItem.setMnemonic('C');
 185       outputTextboxMenu.setMnemonic('T');
 186       undoMenuItem.setMnemonic('Z');
 187       redoMenuItem.setMnemonic('0');
 188       copy.setMnemonic('C');
 189       cut.setMnemonic('U');
 190       pasteMenu.setMnemonic('P');
 191       reload.setMnemonic('R');
 192     }
 193
 194     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 195     {
 196       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 197           getUserColourSchemes().keys();
 198
 199       while (userColours.hasMoreElements())
 200       {
 201         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 202             userColours.
 203             nextElement().toString());
 204         radioItem.setName("USER_DEFINED");
 205         radioItem.addMouseListener(new MouseAdapter()
 206         {
 207           public void mousePressed(MouseEvent evt)
 208           {
 209             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 210             {
 211               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 212
 213               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
 214                   Desktop.desktop,
 215                   "Remove from default list?",
 216                   "Remove user defined colour",
 217                   JOptionPane.YES_NO_OPTION);
 218               if (option == JOptionPane.YES_OPTION)
 219               {
 220                 jalview.gui.UserDefinedColours.removeColourFromDefaults(
 221                     radioItem.getText());
 222                 colourMenu.remove(radioItem);
 223               }
 224               else
 225               {
 226                 radioItem.addActionListener(new ActionListener()
 227                 {
 228                   public void actionPerformed(ActionEvent evt)
 229                   {
 230                     userDefinedColour_actionPerformed(evt);
 231                   }
 232                 });
 233               }
 234             }
 235           }
 236         });
 237         radioItem.addActionListener(new ActionListener()
 238         {
 239           public void actionPerformed(ActionEvent evt)
 240           {
 241             userDefinedColour_actionPerformed(evt);
 242           }
 243         });
 244         colourMenu.insert(radioItem, 15);
 245         colours.add(radioItem);
 246       }
 247     }
 248     colours.add(noColourmenuItem);
 249     colours.add(clustalColour);
 250     colours.add(zappoColour);
 251     colours.add(taylorColour);
 252     colours.add(hydrophobicityColour);
 253     colours.add(helixColour);
 254     colours.add(strandColour);
 255     colours.add(turnColour);
 256     colours.add(buriedColour);
 257     colours.add(userDefinedColour);
 258     colours.add(PIDColour);
 259     colours.add(BLOSUM62Colour);
 260     colours.add(nucleotideColour);
 261
 262     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 263
 264   }
 265
 266   public void setColourSelected(String defaultColour)
 267   {
 268
 269     if (defaultColour != null)
 270     {
 271       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
 272
 273       switch (index)
 274       {
 275         case ColourSchemeProperty.NONE:
 276           noColourmenuItem.setSelected(true);
 277           break;
 278         case ColourSchemeProperty.CLUSTAL:
 279           clustalColour.setSelected(true);
 280
 281           break;
 282
 283         case ColourSchemeProperty.BLOSUM:
 284           BLOSUM62Colour.setSelected(true);
 285
 286           break;
 287
 288         case ColourSchemeProperty.PID:
 289           PIDColour.setSelected(true);
 290
 291           break;
 292
 293         case ColourSchemeProperty.ZAPPO:
 294           zappoColour.setSelected(true);
 295
 296           break;
 297
 298         case ColourSchemeProperty.TAYLOR:
 299           taylorColour.setSelected(true);
 300           break;
 301
 302         case ColourSchemeProperty.HYDROPHOBIC:
 303           hydrophobicityColour.setSelected(true);
 304
 305           break;
 306
 307         case ColourSchemeProperty.HELIX:
 308           helixColour.setSelected(true);
 309
 310           break;
 311
 312         case ColourSchemeProperty.STRAND:
 313           strandColour.setSelected(true);
 314
 315           break;
 316
 317         case ColourSchemeProperty.TURN:
 318           turnColour.setSelected(true);
 319
 320           break;
 321
 322         case ColourSchemeProperty.BURIED:
 323           buriedColour.setSelected(true);
 324
 325           break;
 326
 327         case ColourSchemeProperty.NUCLEOTIDE:
 328           nucleotideColour.setSelected(true);
 329
 330           break;
 331
 332         case ColourSchemeProperty.USER_DEFINED:
 333           userDefinedColour.setSelected(true);
 334
 335           break;
 336       }
 337     }
 338
 339   }
 340
 341   private void jbInit()
 342       throws Exception
 343   {
 344     fileMenu.setText("File");
 345     saveAs.setText("Save As...");
 346     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
 347         KeyEvent.VK_S,
 348         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
 349         java.awt.event.KeyEvent.SHIFT_MASK, false));
 350     saveAs.addActionListener(new ActionListener()
 351     {
 352       public void actionPerformed(ActionEvent e)
 353       {
 354         saveAs_actionPerformed(e);
 355       }
 356     });
 357     closeMenuItem.setText("Close");
 358     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 359         event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 360     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 361     {
 362       public void actionPerformed(ActionEvent e)
 363       {
 364         closeMenuItem_actionPerformed(false);
 365       }
 366     });
 367     editMenu.setText("Edit");
 368     viewMenu.setText("View");
 369     colourMenu.setText("Colour");
 370     calculateMenu.setText("Calculate");
 371     webService.setText("Web Service");
 372     selectAllSequenceMenuItem.setText("Select All");
 373     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 374         java.awt.event.KeyEvent.VK_A,
 375         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 376     selectAllSequenceMenuItem.addActionListener(new java.awt.event.
 377                                                 ActionListener()
 378     {
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         selectAllSequenceMenuItem_actionPerformed(e);
 382       }
 383     });
 384     deselectAllSequenceMenuItem.setText("Deselect All");
 385     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
 386                                                getKeyStroke(
 387         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 388     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
 389                                                   ActionListener()
 390     {
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         deselectAllSequenceMenuItem_actionPerformed(e);
 394       }
 395     });
 396     invertSequenceMenuItem.setText("Invert Sequence Selection");
 397     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 398         java.awt.event.KeyEvent.VK_I,
 399         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 400     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 401     {
 402       public void actionPerformed(ActionEvent e)
 403       {
 404         invertSequenceMenuItem_actionPerformed(e);
 405       }
 406     });
 407     remove2LeftMenuItem.setText("Remove Left");
 408     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
 409         awt.event.KeyEvent.VK_L,
 410         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 411     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 412     {
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         remove2LeftMenuItem_actionPerformed(e);
 416       }
 417     });
 418     remove2RightMenuItem.setText("Remove Right");
 419     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
 420         awt.event.KeyEvent.VK_R,
 421         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 422     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 423     {
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         remove2RightMenuItem_actionPerformed(e);
 427       }
 428     });
 429     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 430     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
 431                                               getKeyStroke(java.awt.event.
 432         KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 433     removeGappedColumnMenuItem.addActionListener(new java.awt.event.
 434                                                  ActionListener()
 435     {
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         removeGappedColumnMenuItem_actionPerformed(e);
 439       }
 440     });
 441     removeAllGapsMenuItem.setText("Remove All Gaps");
 442     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 443         java.awt.event.KeyEvent.VK_E,
 444         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
 445         java.awt.event.KeyEvent.SHIFT_MASK, false));
 446     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 447     {
 448       public void actionPerformed(ActionEvent e)
 449       {
 450         removeAllGapsMenuItem_actionPerformed(e);
 451       }
 452     });
 453     viewBoxesMenuItem.setText("Boxes");
 454     viewBoxesMenuItem.setState(true);
 455     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 456     {
 457       public void actionPerformed(ActionEvent e)
 458       {
 459         viewBoxesMenuItem_actionPerformed(e);
 460       }
 461     });
 462     viewTextMenuItem.setText("Text");
 463     viewTextMenuItem.setState(true);
 464     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 465     {
 466       public void actionPerformed(ActionEvent e)
 467       {
 468         viewTextMenuItem_actionPerformed(e);
 469       }
 470     });
 471     sortPairwiseMenuItem.setText("by Pairwise Identity");
 472     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 473     {
 474       public void actionPerformed(ActionEvent e)
 475       {
 476         sortPairwiseMenuItem_actionPerformed(e);
 477       }
 478     });
 479     sortIDMenuItem.setText("by ID");
 480     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 481     {
 482       public void actionPerformed(ActionEvent e)
 483       {
 484         sortIDMenuItem_actionPerformed(e);
 485       }
 486     });
 487     sortGroupMenuItem.setText("by Group");
 488     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 489     {
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         sortGroupMenuItem_actionPerformed(e);
 493       }
 494     });
 495     removeRedundancyMenuItem.setText("Remove Redundancy...");
 496     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 497         java.awt.event.KeyEvent.VK_D,
 498         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 499     removeRedundancyMenuItem.addActionListener(new java.awt.event.
 500                                                ActionListener()
 501     {
 502       public void actionPerformed(ActionEvent e)
 503       {
 504         removeRedundancyMenuItem_actionPerformed(e);
 505       }
 506     });
 507     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 508     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
 509                                                 ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         pairwiseAlignmentMenuItem_actionPerformed(e);
 514       }
 515     });
 516     PCAMenuItem.setText("Principal Component Analysis");
 517     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 518     {
 519       public void actionPerformed(ActionEvent e)
 520       {
 521         PCAMenuItem_actionPerformed(e);
 522       }
 523     });
 524     averageDistanceTreeMenuItem.setText(
 525         "Average Distance Using % Identity");
 526     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
 527                                                   ActionListener()
 528     {
 529       public void actionPerformed(ActionEvent e)
 530       {
 531         averageDistanceTreeMenuItem_actionPerformed(e);
 532       }
 533     });
 534     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 535     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 536     {
 537       public void actionPerformed(ActionEvent e)
 538       {
 539         neighbourTreeMenuItem_actionPerformed(e);
 540       }
 541     });
 542     this.getContentPane().setLayout(borderLayout1);
 543     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 544     statusBar.setBackground(Color.white);
 545     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 546     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 547     statusBar.setText("Status bar");
 548     outputTextboxMenu.setText("Output to Textbox");
 549     clustalColour.setText("Clustalx");
 550
 551     clustalColour.addActionListener(new java.awt.event.ActionListener()
 552     {
 553       public void actionPerformed(ActionEvent e)
 554       {
 555         clustalColour_actionPerformed(e);
 556       }
 557     });
 558     zappoColour.setText("Zappo");
 559     zappoColour.addActionListener(new java.awt.event.ActionListener()
 560     {
 561       public void actionPerformed(ActionEvent e)
 562       {
 563         zappoColour_actionPerformed(e);
 564       }
 565     });
 566     taylorColour.setText("Taylor");
 567     taylorColour.addActionListener(new java.awt.event.ActionListener()
 568     {
 569       public void actionPerformed(ActionEvent e)
 570       {
 571         taylorColour_actionPerformed(e);
 572       }
 573     });
 574     hydrophobicityColour.setText("Hydrophobicity");
 575     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 576     {
 577       public void actionPerformed(ActionEvent e)
 578       {
 579         hydrophobicityColour_actionPerformed(e);
 580       }
 581     });
 582     helixColour.setText("Helix Propensity");
 583     helixColour.addActionListener(new java.awt.event.ActionListener()
 584     {
 585       public void actionPerformed(ActionEvent e)
 586       {
 587         helixColour_actionPerformed(e);
 588       }
 589     });
 590     strandColour.setText("Strand Propensity");
 591     strandColour.addActionListener(new java.awt.event.ActionListener()
 592     {
 593       public void actionPerformed(ActionEvent e)
 594       {
 595         strandColour_actionPerformed(e);
 596       }
 597     });
 598     turnColour.setText("Turn Propensity");
 599     turnColour.addActionListener(new java.awt.event.ActionListener()
 600     {
 601       public void actionPerformed(ActionEvent e)
 602       {
 603         turnColour_actionPerformed(e);
 604       }
 605     });
 606     buriedColour.setText("Buried Index");
 607     buriedColour.addActionListener(new java.awt.event.ActionListener()
 608     {
 609       public void actionPerformed(ActionEvent e)
 610       {
 611         buriedColour_actionPerformed(e);
 612       }
 613     });
 614     userDefinedColour.setText("User Defined...");
 615     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 616     {
 617       public void actionPerformed(ActionEvent e)
 618       {
 619         userDefinedColour_actionPerformed(e);
 620       }
 621     });
 622     PIDColour.setText("Percentage Identity");
 623     PIDColour.addActionListener(new java.awt.event.ActionListener()
 624     {
 625       public void actionPerformed(ActionEvent e)
 626       {
 627         PIDColour_actionPerformed(e);
 628       }
 629     });
 630     BLOSUM62Colour.setText("BLOSUM62 Score");
 631     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 632     {
 633       public void actionPerformed(ActionEvent e)
 634       {
 635         BLOSUM62Colour_actionPerformed(e);
 636       }
 637     });
 638     avDistanceTreeBlosumMenuItem.setText(
 639         "Average Distance Using BLOSUM62");
 640     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
 641         ActionListener()
 642     {
 643       public void actionPerformed(ActionEvent e)
 644       {
 645         avTreeBlosumMenuItem_actionPerformed(e);
 646       }
 647     });
 648     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 649     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 650     {
 651       public void actionPerformed(ActionEvent e)
 652       {
 653         njTreeBlosumMenuItem_actionPerformed(e);
 654       }
 655     });
 656     annotationPanelMenuItem.setActionCommand("");
 657     annotationPanelMenuItem.setText("Show Annotations");
 658     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 659         "SHOW_ANNOTATIONS", true));
 660     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 661     {
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         annotationPanelMenuItem_actionPerformed(e);
 665       }
 666     });
 667     colourTextMenuItem.setText("Colour Text");
 668     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         colourTextMenuItem_actionPerformed(e);
 673       }
 674     });
 675     htmlMenuItem.setText("HTML");
 676     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 677     {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         htmlMenuItem_actionPerformed(e);
 681       }
 682     });
 683     overviewMenuItem.setText("Overview Window");
 684     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 685     {
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         overviewMenuItem_actionPerformed(e);
 689       }
 690     });
 691     undoMenuItem.setEnabled(false);
 692     undoMenuItem.setText("Undo");
 693     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 694         java.awt.event.KeyEvent.VK_Z,
 695         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 696     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 697     {
 698       public void actionPerformed(ActionEvent e)
 699       {
 700         undoMenuItem_actionPerformed(e);
 701       }
 702     });
 703     redoMenuItem.setEnabled(false);
 704     redoMenuItem.setText("Redo");
 705     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 706         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 707     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 708     {
 709       public void actionPerformed(ActionEvent e)
 710       {
 711         redoMenuItem_actionPerformed(e);
 712       }
 713     });
 714     conservationMenuItem.setText("By Conservation");
 715     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 716     {
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         conservationMenuItem_actionPerformed(e);
 720       }
 721     });
 722     noColourmenuItem.setText("None");
 723     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 724     {
 725       public void actionPerformed(ActionEvent e)
 726       {
 727         noColourmenuItem_actionPerformed(e);
 728       }
 729     });
 730     wrapMenuItem.setText("Wrap");
 731     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 732     {
 733       public void actionPerformed(ActionEvent e)
 734       {
 735         wrapMenuItem_actionPerformed(e);
 736       }
 737     });
 738     printMenuItem.setText("Print ...");
 739     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 740         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 741     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 742     {
 743       public void actionPerformed(ActionEvent e)
 744       {
 745         printMenuItem_actionPerformed(e);
 746       }
 747     });
 748     renderGapsMenuItem.setText("Show Gaps");
 749     renderGapsMenuItem.setState(true);
 750     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 751     {
 752       public void actionPerformed(ActionEvent e)
 753       {
 754         renderGapsMenuItem_actionPerformed(e);
 755       }
 756     });
 757     findMenuItem.setText("Find...");
 758     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 759         java.awt.event.KeyEvent.VK_F,
 760         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 761     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         findMenuItem_actionPerformed(e);
 766       }
 767     });
 768     abovePIDThreshold.setText("Above Identity Threshold");
 769     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 770     {
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         abovePIDThreshold_actionPerformed(e);
 774       }
 775     });
 776     showSeqFeatures.setText("Show Sequence Features");
 777     showSeqFeatures.addActionListener(new ActionListener()
 778     {
 779       public void actionPerformed(ActionEvent actionEvent)
 780       {
 781         showSeqFeatures_actionPerformed(actionEvent);
 782       }
 783     });
 784     nucleotideColour.setText("Nucleotide");
 785     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 786     {
 787       public void actionPerformed(ActionEvent e)
 788       {
 789         nucleotideColour_actionPerformed(e);
 790       }
 791     });
 792     deleteGroups.setText("Undefine groups");
 793     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 794         event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 795     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 796     {
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         deleteGroups_actionPerformed(e);
 800       }
 801     });
 802     copy.setText("Copy");
 803     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 804         java.awt.event.KeyEvent.VK_C,
 805         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 806
 807     copy.addActionListener(new java.awt.event.ActionListener()
 808     {
 809       public void actionPerformed(ActionEvent e)
 810       {
 811         copy_actionPerformed(e);
 812       }
 813     });
 814     cut.setText("Cut");
 815     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 816         java.awt.event.KeyEvent.VK_X,
 817         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 818     cut.addActionListener(new java.awt.event.ActionListener()
 819     {
 820       public void actionPerformed(ActionEvent e)
 821       {
 822         cut_actionPerformed(e);
 823       }
 824     });
 825     delete.setText("Delete");
 826     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
 827         KeyEvent.VK_BACK_SPACE, 0, false));
 828     delete.addActionListener(new java.awt.event.ActionListener()
 829     {
 830       public void actionPerformed(ActionEvent e)
 831       {
 832         delete_actionPerformed(e);
 833       }
 834     });
 835     pasteMenu.setText("Paste");
 836     pasteNew.setText("To New Alignment");
 837     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 838         java.awt.event.KeyEvent.VK_V,
 839         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
 840         java.awt.event.KeyEvent.SHIFT_MASK, false));
 841     pasteNew.addActionListener(new java.awt.event.ActionListener()
 842     {
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         pasteNew_actionPerformed(e);
 846       }
 847     });
 848     pasteThis.setText("Add To This Alignment");
 849     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 850         java.awt.event.KeyEvent.VK_V,
 851         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 852     pasteThis.addActionListener(new java.awt.event.ActionListener()
 853     {
 854       public void actionPerformed(ActionEvent e)
 855       {
 856         pasteThis_actionPerformed(e);
 857       }
 858     });
 859     applyToAllGroups.setText("Apply Colour To All Groups");
 860     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 861     {
 862       public void actionPerformed(ActionEvent e)
 863       {
 864         applyToAllGroups_actionPerformed(e);
 865       }
 866     });
 867     createPNG.addActionListener(new java.awt.event.ActionListener()
 868     {
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         createPNG(null);
 872       }
 873     });
 874     createPNG.setActionCommand("Save As PNG Image");
 875     createPNG.setText("PNG");
 876     font.setText("Font...");
 877     font.addActionListener(new java.awt.event.ActionListener()
 878     {
 879       public void actionPerformed(ActionEvent e)
 880       {
 881         font_actionPerformed(e);
 882       }
 883     });
 884
 885     seqLimits.setText("Show Sequence Limits");
 886     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
 887     seqLimits.addActionListener(new java.awt.event.ActionListener()
 888     {
 889       public void actionPerformed(ActionEvent e)
 890       {
 891         seqLimit_actionPerformed(e);
 892       }
 893     });
 894     epsFile.setText("EPS");
 895     epsFile.addActionListener(new java.awt.event.ActionListener()
 896     {
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         createEPS(null);
 900       }
 901     });
 902     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 903     LoadtreeMenuItem.setText("Load Associated Tree");
 904     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 905     {
 906       public void actionPerformed(ActionEvent e)
 907       {
 908         LoadtreeMenuItem_actionPerformed(e);
 909       }
 910     });
 911     scaleAbove.setVisible(false);
 912     scaleAbove.setText("Scale Above");
 913     scaleAbove.addActionListener(new java.awt.event.ActionListener()
 914     {
 915       public void actionPerformed(ActionEvent e)
 916       {
 917         scaleAbove_actionPerformed(e);
 918       }
 919     });
 920     scaleLeft.setVisible(false);
 921     scaleLeft.setSelected(true);
 922     scaleLeft.setText("Scale Left");
 923     scaleLeft.addActionListener(new java.awt.event.ActionListener()
 924     {
 925       public void actionPerformed(ActionEvent e)
 926       {
 927         scaleLeft_actionPerformed(e);
 928       }
 929     });
 930     scaleRight.setVisible(false);
 931     scaleRight.setSelected(true);
 932     scaleRight.setText("Scale Right");
 933     scaleRight.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         scaleRight_actionPerformed(e);
 938       }
 939     });
 940     centreColumnLabelsMenuItem.setVisible(true);
 941     centreColumnLabelsMenuItem.setState(false);
 942     centreColumnLabelsMenuItem.setText("Centre Column Labels");
 943     centreColumnLabelsMenuItem.addActionListener(new java.awt.event.ActionListener()
 944     {
 945       public void actionPerformed(ActionEvent e)
 946       {
 947         centreColumnLabels_actionPerformed(e);
 948       }
 949     });
 950
 951     modifyPID.setText("Modify Identity Threshold...");
 952     modifyPID.addActionListener(new java.awt.event.ActionListener()
 953     {
 954       public void actionPerformed(ActionEvent e)
 955       {
 956         modifyPID_actionPerformed(e);
 957       }
 958     });
 959     modifyConservation.setText("Modify Conservation Threshold...");
 960     modifyConservation.addActionListener(new java.awt.event.ActionListener()
 961     {
 962       public void actionPerformed(ActionEvent e)
 963       {
 964         modifyConservation_actionPerformed(e);
 965       }
 966     });
 967     sortByTreeMenu.setText("By Tree Order");
 968     sort.setText("Sort");
 969     sort.addMenuListener(new MenuListener()
 970     {
 971       public void menuSelected(MenuEvent e)
 972       {
 973         buildTreeMenu();
 974       }
 975
 976       public void menuDeselected(MenuEvent e)
 977       {
 978       }
 979
 980       public void menuCanceled(MenuEvent e)
 981       {
 982       }
 983     });
 984     sortByAnnotScore.setText("by Score");
 985     sort.add(sortByAnnotScore);
 986     sortByAnnotScore.addMenuListener(
 987             new javax.swing.event.MenuListener() {
 988
 989                 public void menuCanceled(MenuEvent e)
 990                 {
 991                 }
 992
 993                 public void menuDeselected(MenuEvent e)
 994                 {
 995                 }
 996
 997                 public void menuSelected(MenuEvent e)
 998                 {
 999                   buildSortByAnnotationScoresMenu();
1000                 }
1001               }
1002               );
1003     sortByAnnotScore.setVisible(false);
1004
1005     calculate.setText("Calculate Tree");
1006
1007     jMenu2.setText("Export Image");
1008     padGapsMenuitem.setText("Pad Gaps");
1009     padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1010     padGapsMenuitem.addActionListener(new ActionListener()
1011     {
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         padGapsMenuitem_actionPerformed(e);
1015       }
1016     });
1017     vamsasStore.setVisible(false);
1018     vamsasStore.setText("VAMSAS store");
1019     vamsasStore.addActionListener(new ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         vamsasStore_actionPerformed(e);
1024       }
1025     });
1026     showTranslation.setText("Translate cDNA");
1027     showTranslation.addActionListener(new ActionListener()
1028     {
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         showTranslation_actionPerformed(e);
1032       }
1033     });
1034     extractScores.setText("Extract Scores...");
1035     extractScores.addActionListener(new ActionListener()
1036     {
1037       public void actionPerformed(ActionEvent e)
1038       {
1039         extractScores_actionPerformed(e);
1040       }
1041     });
1042     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
1043     showProducts.setText("Get Cross References");
1044     /*showProducts.addActionListener(new ActionListener()
1045     {
1046
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         showProducts_actionPerformed(e);
1050       }
1051     });*/
1052     featureSettings.setText("Feature Settings...");
1053     featureSettings.addActionListener(new ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         featureSettings_actionPerformed(e);
1058       }
1059     });
1060     fetchSequence.setText("Fetch Sequence(s)...");
1061     fetchSequence.addActionListener(new ActionListener()
1062     {
1063       public void actionPerformed(ActionEvent e)
1064       {
1065         fetchSequence_actionPerformed(e);
1066       }
1067     });
1068
1069     annotationColour.setText("By Annotation...");
1070     annotationColour.addActionListener(new ActionListener()
1071     {
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         annotationColour_actionPerformed(e);
1075       }
1076     });
1077     associatedData.setText("Load Features / Annotations");
1078     associatedData.addActionListener(new ActionListener()
1079     {
1080       public void actionPerformed(ActionEvent e)
1081       {
1082         associatedData_actionPerformed(e);
1083       }
1084     });
1085     autoCalculate.setText("Autocalculate Consensus");
1086     autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1087     autoCalculate.addActionListener(new ActionListener()
1088     {
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         autoCalculate_actionPerformed(e);
1092       }
1093     });
1094     addSequenceMenu.setText("Add Sequences");
1095     addFromFile.setText("From File");
1096     addFromFile.addActionListener(new ActionListener()
1097     {
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         addFromFile_actionPerformed(e);
1101       }
1102     });
1103     addFromText.setText("From Textbox");
1104     addFromText.addActionListener(new ActionListener()
1105     {
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         addFromText_actionPerformed(e);
1109       }
1110     });
1111     addFromURL.setText("From URL");
1112     addFromURL.addActionListener(new ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         addFromURL_actionPerformed(e);
1117       }
1118     });
1119     exportFeatures.setText("Export Features...");
1120     exportFeatures.addActionListener(new ActionListener()
1121     {
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         exportFeatures_actionPerformed(e);
1125       }
1126     });
1127     exportAnnotations.setText("Export Annotations...");
1128     exportAnnotations.addActionListener(new ActionListener()
1129     {
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         exportAnnotations_actionPerformed(e);
1133       }
1134     });
1135     statusPanel.setLayout(gridLayout1);
1136     jMenu3.setText("Show");
1137     showAllSeqs.setText("All Sequences");
1138     showAllSeqs.addActionListener(new ActionListener()
1139     {
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         showAllSeqs_actionPerformed(e);
1143       }
1144     });
1145     showAllColumns.setText("All Columns");
1146     showAllColumns.addActionListener(new ActionListener()
1147     {
1148       public void actionPerformed(ActionEvent e)
1149       {
1150         showAllColumns_actionPerformed(e);
1151       }
1152     });
1153     hideMenu.setText("Hide");
1154     hideSelSequences.setText("Selected Sequences");
1155     hideSelSequences.addActionListener(new ActionListener()
1156     {
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         hideSelSequences_actionPerformed(e);
1160       }
1161     });
1162     hideSelColumns.setText("Selected Columns");
1163     hideSelColumns.addActionListener(new ActionListener()
1164     {
1165       public void actionPerformed(ActionEvent e)
1166       {
1167         hideSelColumns_actionPerformed(e);
1168       }
1169     });
1170     hiddenMarkers.setText("Show Hidden Markers");
1171     hiddenMarkers.addActionListener(new ActionListener()
1172     {
1173       public void actionPerformed(ActionEvent e)
1174       {
1175         hiddenMarkers_actionPerformed(e);
1176       }
1177     });
1178     invertColSel.setText("Invert Column Selection");
1179     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1180         event.KeyEvent.VK_I,
1181         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1182         | java.awt.event.KeyEvent.ALT_MASK,
1183         false));
1184     invertColSel.addActionListener(new ActionListener()
1185     {
1186       public void actionPerformed(ActionEvent e)
1187       {
1188         invertColSel_actionPerformed(e);
1189       }
1190     });
1191     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1192     {
1193       public void stateChanged(ChangeEvent evt)
1194       {
1195         JTabbedPane pane = (JTabbedPane) evt.getSource();
1196         int sel = pane.getSelectedIndex();
1197         tabSelectionChanged(sel);
1198       }
1199     });
1200     tabbedPane.addMouseListener(new MouseAdapter()
1201     {
1202       public void mousePressed(MouseEvent e)
1203       {
1204         tabbedPane_mousePressed(e);
1205       }
1206     });
1207     tabbedPane.addFocusListener(new FocusAdapter()
1208     {
1209       public void focusGained(FocusEvent e)
1210       {
1211         tabbedPane_focusGained(e);
1212       }
1213     });
1214     save.setText("Save");
1215     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1216         KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1217     save.addActionListener(new ActionListener()
1218     {
1219       public void actionPerformed(ActionEvent e)
1220       {
1221         save_actionPerformed(e);
1222       }
1223     });
1224     reload.setEnabled(false);
1225     reload.setText("Reload");
1226     reload.addActionListener(new ActionListener()
1227     {
1228       public void actionPerformed(ActionEvent e)
1229       {
1230         reload_actionPerformed(e);
1231       }
1232     });
1233     newView.setText("New View");
1234     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
1235         KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
1236     newView.addActionListener(new ActionListener()
1237     {
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         newView_actionPerformed(e);
1241       }
1242     });
1243     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1244                               +
1245         "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1246     textColour.setText("Colour Text ...");
1247     textColour.addActionListener(new ActionListener()
1248     {
1249       public void actionPerformed(ActionEvent e)
1250       {
1251         textColour_actionPerformed(e);
1252       }
1253     });
1254     formatMenu.setText("Format");
1255     selectMenu.setText("Select");
1256     idRightAlign.setText("Right Align Sequence Id");
1257     idRightAlign.addActionListener(new ActionListener()
1258     {
1259       public void actionPerformed(ActionEvent e)
1260       {
1261         idRightAlign_actionPerformed(e);
1262       }
1263     });
1264     gatherViews.setEnabled(false);
1265     gatherViews.setText("Gather Views");
1266     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1267         event.KeyEvent.VK_G, 0, false));
1268     gatherViews.addActionListener(new ActionListener()
1269     {
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         gatherViews_actionPerformed(e);
1273       }
1274     });
1275     expandViews.setEnabled(false);
1276     expandViews.setText("Expand Views");
1277     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
1278         event.KeyEvent.VK_X, 0, false));
1279     expandViews.addActionListener(new ActionListener()
1280     {
1281       public void actionPerformed(ActionEvent e)
1282       {
1283         expandViews_actionPerformed(e);
1284       }
1285     });
1286     pageSetup.setText("Page Setup ...");
1287     pageSetup.addActionListener(new ActionListener()
1288     {
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         pageSetup_actionPerformed(e);
1292       }
1293     });
1294     alignmentProperties.setText("Alignment Properties...");
1295     alignmentProperties.addActionListener(new ActionListener()
1296     {
1297       public void actionPerformed(ActionEvent actionEvent)
1298       {
1299         alignmentProperties();
1300       }
1301     });
1302
1303     alignFrameMenuBar.add(fileMenu);
1304     alignFrameMenuBar.add(editMenu);
1305     alignFrameMenuBar.add(selectMenu);
1306     alignFrameMenuBar.add(viewMenu);
1307     alignFrameMenuBar.add(formatMenu);
1308     alignFrameMenuBar.add(colourMenu);
1309     alignFrameMenuBar.add(calculateMenu);
1310     alignFrameMenuBar.add(webService);
1311     fileMenu.add(fetchSequence);
1312     fileMenu.add(addSequenceMenu);
1313     fileMenu.add(reload);
1314     fileMenu.addSeparator();
1315     fileMenu.add(vamsasStore);
1316     fileMenu.add(save);
1317     fileMenu.add(saveAs);
1318     fileMenu.add(outputTextboxMenu);
1319     fileMenu.add(pageSetup);
1320     fileMenu.add(printMenuItem);
1321     fileMenu.addSeparator();
1322     fileMenu.add(jMenu2);
1323     fileMenu.add(exportFeatures);
1324     fileMenu.add(exportAnnotations);
1325     fileMenu.add(LoadtreeMenuItem);
1326     fileMenu.add(associatedData);
1327     fileMenu.addSeparator();
1328     fileMenu.add(closeMenuItem);
1329     editMenu.add(undoMenuItem);
1330     editMenu.add(redoMenuItem);
1331     editMenu.add(cut);
1332     editMenu.add(copy);
1333     editMenu.add(pasteMenu);
1334     editMenu.add(delete);
1335     editMenu.addSeparator();
1336     editMenu.add(remove2LeftMenuItem);
1337     editMenu.add(remove2RightMenuItem);
1338     editMenu.add(removeGappedColumnMenuItem);
1339     editMenu.add(removeAllGapsMenuItem);
1340     editMenu.add(removeRedundancyMenuItem);
1341     editMenu.addSeparator();
1342     editMenu.add(padGapsMenuitem);
1343     viewMenu.add(newView);
1344     viewMenu.add(expandViews);
1345     viewMenu.add(gatherViews);
1346     viewMenu.addSeparator();
1347     viewMenu.add(jMenu3);
1348     viewMenu.add(hideMenu);
1349     viewMenu.addSeparator();
1350     viewMenu.add(annotationPanelMenuItem);
1351     viewMenu.addSeparator();
1352     viewMenu.add(showSeqFeatures);
1353     viewMenu.add(featureSettings);
1354     viewMenu.addSeparator();
1355     viewMenu.add(alignmentProperties);
1356     viewMenu.addSeparator();
1357     viewMenu.add(overviewMenuItem);
1358     colourMenu.add(applyToAllGroups);
1359     colourMenu.add(textColour);
1360     colourMenu.addSeparator();
1361     colourMenu.add(noColourmenuItem);
1362     colourMenu.add(clustalColour);
1363     colourMenu.add(BLOSUM62Colour);
1364     colourMenu.add(PIDColour);
1365     colourMenu.add(zappoColour);
1366     colourMenu.add(taylorColour);
1367     colourMenu.add(hydrophobicityColour);
1368     colourMenu.add(helixColour);
1369     colourMenu.add(strandColour);
1370     colourMenu.add(turnColour);
1371     colourMenu.add(buriedColour);
1372     colourMenu.add(nucleotideColour);
1373     colourMenu.add(userDefinedColour);
1374     colourMenu.addSeparator();
1375     colourMenu.add(conservationMenuItem);
1376     colourMenu.add(modifyConservation);
1377     colourMenu.add(abovePIDThreshold);
1378     colourMenu.add(modifyPID);
1379     colourMenu.add(annotationColour);
1380     calculateMenu.add(sort);
1381     calculateMenu.add(calculate);
1382     calculateMenu.addSeparator();
1383     calculateMenu.add(pairwiseAlignmentMenuItem);
1384     calculateMenu.add(PCAMenuItem);
1385     calculateMenu.addSeparator();
1386     calculateMenu.add(showTranslation);
1387     calculateMenu.add(showProducts);
1388     calculateMenu.add(autoCalculate);
1389     calculateMenu.addSeparator();
1390     calculateMenu.add(extractScores);
1391     webServiceNoServices = new JMenuItem("<No Services>");
1392     webService.add(webServiceNoServices);
1393     pasteMenu.add(pasteNew);
1394     pasteMenu.add(pasteThis);
1395     sort.add(sortIDMenuItem);
1396     sort.add(sortGroupMenuItem);
1397     sort.add(sortPairwiseMenuItem);
1398     sort.add(sortByTreeMenu);
1399     calculate.add(averageDistanceTreeMenuItem);
1400     calculate.add(neighbourTreeMenuItem);
1401     calculate.add(avDistanceTreeBlosumMenuItem);
1402     calculate.add(njTreeBlosumMenuItem);
1403     jMenu2.add(htmlMenuItem);
1404     jMenu2.add(epsFile);
1405     jMenu2.add(createPNG);
1406     addSequenceMenu.add(addFromFile);
1407     addSequenceMenu.add(addFromText);
1408     addSequenceMenu.add(addFromURL);
1409     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1410     statusPanel.add(statusBar, null);
1411     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1412     jMenu3.add(showAllColumns);
1413     jMenu3.add(showAllSeqs);
1414     hideMenu.add(hideSelColumns);
1415     hideMenu.add(hideSelSequences);
1416     formatMenu.add(font);
1417     formatMenu.addSeparator();
1418     formatMenu.add(wrapMenuItem);
1419     formatMenu.add(scaleAbove);
1420     formatMenu.add(scaleLeft);
1421     formatMenu.add(scaleRight);
1422     formatMenu.add(seqLimits);
1423     formatMenu.add(idRightAlign);
1424     formatMenu.add(hiddenMarkers);
1425     formatMenu.add(viewBoxesMenuItem);
1426     formatMenu.add(viewTextMenuItem);
1427     formatMenu.add(colourTextMenuItem);
1428     formatMenu.add(renderGapsMenuItem);
1429     formatMenu.add(centreColumnLabelsMenuItem);
1430     selectMenu.add(findMenuItem);
1431     selectMenu.addSeparator();
1432     selectMenu.add(selectAllSequenceMenuItem);
1433     selectMenu.add(deselectAllSequenceMenuItem);
1434     selectMenu.add(invertSequenceMenuItem);
1435     selectMenu.add(invertColSel);
1436     selectMenu.add(deleteGroups);
1437   }
1438
1439   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1440   {
1441   }
1442
1443   protected void showProducts_actionPerformed(ActionEvent e)
1444   {
1445   }
1446
1447   protected void buildSortByAnnotationScoresMenu()
1448   {
1449   }
1450
1451   protected void extractScores_actionPerformed(ActionEvent e)
1452   {
1453   }
1454
1455   protected void outputText_actionPerformed(ActionEvent e)
1456   {
1457   }
1458
1459   public void addFromFile_actionPerformed(ActionEvent e)
1460   {
1461
1462   }
1463
1464   public void addFromText_actionPerformed(ActionEvent e)
1465   {
1466
1467   }
1468
1469   public void addFromURL_actionPerformed(ActionEvent e)
1470   {
1471
1472   }
1473
1474   public void exportFeatures_actionPerformed(ActionEvent e)
1475   {
1476
1477   }
1478
1479   public void exportAnnotations_actionPerformed(ActionEvent e)
1480   {
1481
1482   }
1483
1484   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1485   {
1486   }
1487
1488   protected void closeMenuItem_actionPerformed(boolean b)
1489   {
1490   }
1491
1492   protected void redoMenuItem_actionPerformed(ActionEvent e)
1493   {
1494   }
1495
1496   protected void undoMenuItem_actionPerformed(ActionEvent e)
1497   {
1498   }
1499
1500   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1501   {
1502   }
1503
1504   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1505   {
1506   }
1507
1508   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1509   {
1510   }
1511
1512   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1513   {
1514   }
1515
1516   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1517   {
1518   }
1519
1520   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1521   {
1522   }
1523
1524   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1525   {
1526   }
1527
1528   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1529   {
1530   }
1531
1532   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1533   {
1534   }
1535
1536   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1537   {
1538   }
1539
1540   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1541   {
1542   }
1543
1544   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1545   {
1546   }
1547
1548   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1549   {
1550   }
1551
1552   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1553   {
1554   }
1555
1556   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1557   {
1558   }
1559
1560   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1561   {
1562   }
1563
1564   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1565   {
1566   }
1567
1568   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1569   {
1570   }
1571
1572   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1573   {
1574   }
1575
1576   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1577   {
1578   }
1579
1580   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1581   {
1582   }
1583
1584   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1585   {
1586   }
1587
1588   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1589   {
1590   }
1591
1592   protected void clustalColour_actionPerformed(ActionEvent e)
1593   {
1594   }
1595
1596   protected void zappoColour_actionPerformed(ActionEvent e)
1597   {
1598   }
1599
1600   protected void taylorColour_actionPerformed(ActionEvent e)
1601   {
1602   }
1603
1604   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1605   {
1606   }
1607
1608   protected void helixColour_actionPerformed(ActionEvent e)
1609   {
1610   }
1611
1612   protected void strandColour_actionPerformed(ActionEvent e)
1613   {
1614   }
1615
1616   protected void turnColour_actionPerformed(ActionEvent e)
1617   {
1618   }
1619
1620   protected void buriedColour_actionPerformed(ActionEvent e)
1621   {
1622   }
1623
1624   protected void userDefinedColour_actionPerformed(ActionEvent e)
1625   {
1626   }
1627
1628   protected void PIDColour_actionPerformed(ActionEvent e)
1629   {
1630   }
1631
1632   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1633   {
1634   }
1635
1636   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1637   {
1638   }
1639
1640   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1641   {
1642   }
1643
1644   protected void printMenuItem_actionPerformed(ActionEvent e)
1645   {
1646   }
1647
1648   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1649   {
1650   }
1651
1652   protected void findMenuItem_actionPerformed(ActionEvent e)
1653   {
1654   }
1655
1656   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1657   {
1658   }
1659
1660   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1661   {
1662   }
1663
1664   protected void nucleotideColour_actionPerformed(ActionEvent e)
1665   {
1666   }
1667
1668   protected void deleteGroups_actionPerformed(ActionEvent e)
1669   {
1670   }
1671
1672   protected void copy_actionPerformed(ActionEvent e)
1673   {
1674   }
1675
1676   protected void cut_actionPerformed(ActionEvent e)
1677   {
1678   }
1679
1680   protected void delete_actionPerformed(ActionEvent e)
1681   {
1682   }
1683
1684   protected void pasteNew_actionPerformed(ActionEvent e)
1685   {
1686   }
1687
1688   protected void pasteThis_actionPerformed(ActionEvent e)
1689   {
1690   }
1691
1692   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1693   {
1694   }
1695
1696   public void createPNG(java.io.File f)
1697   {
1698   }
1699
1700   protected void font_actionPerformed(ActionEvent e)
1701   {
1702   }
1703
1704   protected void seqLimit_actionPerformed(ActionEvent e)
1705   {
1706   }
1707
1708   public void seqDBRef_actionPerformed(ActionEvent e)
1709   {
1710
1711   }
1712
1713   public void createEPS(java.io.File f)
1714   {
1715   }
1716
1717   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1718   {
1719   }
1720
1721   protected void jpred_actionPerformed(ActionEvent e)
1722   {
1723   }
1724
1725   protected void scaleAbove_actionPerformed(ActionEvent e)
1726   {
1727   }
1728
1729   protected void scaleLeft_actionPerformed(ActionEvent e)
1730   {
1731   }
1732
1733   protected void scaleRight_actionPerformed(ActionEvent e)
1734   {
1735   }
1736
1737   protected void modifyPID_actionPerformed(ActionEvent e)
1738   {
1739   }
1740
1741   protected void modifyConservation_actionPerformed(ActionEvent e)
1742   {
1743   }
1744
1745   protected void saveAs_actionPerformed(ActionEvent e)
1746   {
1747   }
1748
1749   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1750   {
1751   }
1752
1753   public void vamsasStore_actionPerformed(ActionEvent e)
1754   {
1755
1756   }
1757
1758   public void vamsasLoad_actionPerformed(ActionEvent e)
1759   {
1760
1761   }
1762
1763   public void showTranslation_actionPerformed(ActionEvent e)
1764   {
1765
1766   }
1767
1768   public void featureSettings_actionPerformed(ActionEvent e)
1769   {
1770
1771   }
1772
1773   public void fetchSequence_actionPerformed(ActionEvent e)
1774   {
1775
1776   }
1777
1778   public void smoothFont_actionPerformed(ActionEvent e)
1779   {
1780
1781   }
1782
1783   public void annotationColour_actionPerformed(ActionEvent e)
1784   {
1785
1786   }
1787
1788   public void associatedData_actionPerformed(ActionEvent e)
1789   {
1790
1791   }
1792
1793   public void autoCalculate_actionPerformed(ActionEvent e)
1794   {
1795
1796   }
1797
1798   public void showAllSeqs_actionPerformed(ActionEvent e)
1799   {
1800
1801   }
1802
1803   public void showAllColumns_actionPerformed(ActionEvent e)
1804   {
1805
1806   }
1807
1808   public void hideSelSequences_actionPerformed(ActionEvent e)
1809   {
1810
1811   }
1812
1813   public void hideSelColumns_actionPerformed(ActionEvent e)
1814   {
1815
1816   }
1817
1818   public void hiddenMarkers_actionPerformed(ActionEvent e)
1819   {
1820
1821   }
1822
1823   public void findPdbId_actionPerformed(ActionEvent e)
1824   {
1825
1826   }
1827
1828   public void enterPdbId_actionPerformed(ActionEvent e)
1829   {
1830
1831   }
1832
1833   public void pdbFile_actionPerformed(ActionEvent e)
1834   {
1835
1836   }
1837
1838   public void invertColSel_actionPerformed(ActionEvent e)
1839   {
1840
1841   }
1842
1843   public void tabSelectionChanged(int sel)
1844   {
1845
1846   }
1847
1848   public void tabbedPane_mousePressed(MouseEvent e)
1849   {
1850
1851   }
1852
1853   public void tabbedPane_focusGained(FocusEvent e)
1854   {
1855     requestFocus();
1856   }
1857
1858   public void save_actionPerformed(ActionEvent e)
1859   {
1860
1861   }
1862
1863   public void reload_actionPerformed(ActionEvent e)
1864   {
1865
1866   }
1867
1868   public void newView_actionPerformed(ActionEvent e)
1869   {
1870
1871   }
1872
1873   public void textColour_actionPerformed(ActionEvent e)
1874   {
1875
1876   }
1877
1878   public void idRightAlign_actionPerformed(ActionEvent e)
1879   {
1880
1881   }
1882
1883   public void expandViews_actionPerformed(ActionEvent e)
1884   {
1885
1886   }
1887
1888   public void gatherViews_actionPerformed(ActionEvent e)
1889   {
1890
1891   }
1892
1893   public void buildTreeMenu()
1894   {
1895
1896   }
1897
1898   public void pageSetup_actionPerformed(ActionEvent e)
1899   {
1900
1901   }
1902
1903   public void alignmentProperties()
1904   {
1905
1906   }
1907 }