src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 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 import javax.swing.*;
  24
  25 import jalview.schemes.*;
  26 import java.awt.BorderLayout;
  27
  28 public class GAlignFrame
  29     extends JInternalFrame
  30 {
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  32   protected JMenu fileMenu = new JMenu();
  33   protected JMenuItem closeMenuItem = new JMenuItem();
  34   protected JMenu editMenu = new JMenu();
  35   protected JMenu viewMenu = new JMenu();
  36   protected JMenu colourMenu = new JMenu();
  37   protected JMenu calculateMenu = new JMenu();
  38   protected JMenu webService = new JMenu();
  39   protected JMenuItem webServiceNoServices;
  40   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  41   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  42   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  43   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  44   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  45   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  46   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  47   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  48   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  49   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  50   protected JMenuItem sortIDMenuItem = new JMenuItem();
  51   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  54   protected JMenuItem PCAMenuItem = new JMenuItem();
  55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  57   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  58   BorderLayout borderLayout1 = new BorderLayout();
  59   public JLabel statusBar = new JLabel();
  60   protected JMenuItem saveAlignmentMenu = new JMenuItem();
  61   protected JMenu outputTextboxMenu = new JMenu();
  62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  65   protected JRadioButtonMenuItem hydrophobicityColour = new
  66       JRadioButtonMenuItem();
  67   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  68   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  71   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  73   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  74   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  75   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  76   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  77   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  78   JMenuItem htmlMenuItem = new JMenuItem();
  79   JMenuItem overviewMenuItem = new JMenuItem();
  80   protected JMenuItem undoMenuItem = new JMenuItem();
  81   protected JMenuItem redoMenuItem = new JMenuItem();
  82   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  84   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  85   JMenuItem printMenuItem = new JMenuItem();
  86   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  87   JMenuItem findMenuItem = new JMenuItem();
  88   JMenu searchMenu = new JMenu();
  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 jMenu1 = 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   public JMenuItem featureSettings = new JMenuItem();
 119   JMenuItem fetchSequence = new JMenuItem();
 120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
 121   JMenuItem annotationColour = new JMenuItem();
 122   JMenuItem associatedData = new JMenuItem();
 123   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 124   JMenu addSequenceMenu = new JMenu();
 125   JMenuItem addFromFile = new JMenuItem();
 126   JMenuItem addFromText = new JMenuItem();
 127   JMenuItem addFromURL = new JMenuItem();
 128   JMenuItem exportAnnotations = new JMenuItem();
 129   JMenuItem exportFeatures = new JMenuItem();
 130   protected JPanel statusPanel = new JPanel();
 131   GridLayout gridLayout1 = new GridLayout();
 132   JMenu jMenu3 = new JMenu();
 133   JMenuItem showAllSeqs = new JMenuItem();
 134   JMenuItem showAllColumns = new JMenuItem();
 135   JMenu jMenu4 = new JMenu();
 136   JMenuItem hideSelSequences = new JMenuItem();
 137   JMenuItem hideSelColumns = new JMenuItem();
 138   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 139   JMenuItem invertColSel = new JMenuItem();
 140
 141   public GAlignFrame()
 142   {
 143
 144
 145     try
 146     {
 147       jbInit();
 148       setJMenuBar(alignFrameMenuBar);
 149
 150       // dynamically fill save as menu with available formats
 151       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 152       {
 153         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
 154
 155         item.addActionListener(new java.awt.event.ActionListener()
 156         {
 157           public void actionPerformed(ActionEvent e)
 158           {
 159             outputText_actionPerformed(e);
 160           }
 161         });
 162
 163         outputTextboxMenu.add(item);
 164       }
 165     }
 166     catch (Exception e)
 167     {
 168     }
 169
 170
 171     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
 172     {
 173       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 174           getUserColourSchemes().keys();
 175
 176       while (userColours.hasMoreElements())
 177       {
 178         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
 179             nextElement().toString());
 180         radioItem.setName("USER_DEFINED");
 181         radioItem.addMouseListener(new MouseAdapter()
 182             {
 183               public void mousePressed(MouseEvent evt)
 184               {
 185                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 186                 {
 187                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 188
 189                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
 190                       "Remove from default list?",
 191                       "Remove user defined colour",
 192                       JOptionPane.YES_NO_OPTION);
 193                   if(option == JOptionPane.YES_OPTION)
 194                   {
 195                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
 196                     colourMenu.remove(radioItem);
 197                   }
 198                   else
 199                     radioItem.addActionListener(new ActionListener()
 200                     {
 201                       public void actionPerformed(ActionEvent evt)
 202                       {
 203                         userDefinedColour_actionPerformed(evt);
 204                       }
 205                     });
 206                 }
 207               }
 208             });
 209         radioItem.addActionListener(new ActionListener()
 210         {
 211           public void actionPerformed(ActionEvent evt)
 212           {
 213             userDefinedColour_actionPerformed(evt);
 214           }
 215         });
 216         colourMenu.insert(radioItem, 15);
 217         colours.add(radioItem);
 218       }
 219     }
 220     colours.add(noColourmenuItem);
 221     colours.add(clustalColour);
 222     colours.add(zappoColour);
 223     colours.add(taylorColour);
 224     colours.add(hydrophobicityColour);
 225     colours.add(helixColour);
 226     colours.add(strandColour);
 227     colours.add(turnColour);
 228     colours.add(buriedColour);
 229     colours.add(userDefinedColour);
 230     colours.add(PIDColour);
 231     colours.add(BLOSUM62Colour);
 232     colours.add(nucleotideColour);
 233
 234     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 235
 236
 237   }
 238
 239   public void setColourSelected(String defaultColour)
 240   {
 241
 242     if (defaultColour != null)
 243     {
 244       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
 245
 246       switch (index)
 247       {
 248         case ColourSchemeProperty.NONE:
 249               noColourmenuItem.setSelected(true);
 250               break;
 251         case ColourSchemeProperty.CLUSTAL:
 252           clustalColour.setSelected(true);
 253
 254           break;
 255
 256         case ColourSchemeProperty.BLOSUM:
 257           BLOSUM62Colour.setSelected(true);
 258
 259           break;
 260
 261         case ColourSchemeProperty.PID:
 262           PIDColour.setSelected(true);
 263
 264           break;
 265
 266         case ColourSchemeProperty.ZAPPO:
 267           zappoColour.setSelected(true);
 268
 269           break;
 270
 271         case ColourSchemeProperty.TAYLOR:
 272           taylorColour.setSelected(true);
 273           break;
 274
 275         case ColourSchemeProperty.HYDROPHOBIC:
 276           hydrophobicityColour.setSelected(true);
 277
 278           break;
 279
 280         case ColourSchemeProperty.HELIX:
 281           helixColour.setSelected(true);
 282
 283           break;
 284
 285         case ColourSchemeProperty.STRAND:
 286           strandColour.setSelected(true);
 287
 288           break;
 289
 290         case ColourSchemeProperty.TURN:
 291           turnColour.setSelected(true);
 292
 293           break;
 294
 295         case ColourSchemeProperty.BURIED:
 296           buriedColour.setSelected(true);
 297
 298           break;
 299
 300         case ColourSchemeProperty.NUCLEOTIDE:
 301           nucleotideColour.setSelected(true);
 302
 303           break;
 304
 305         case ColourSchemeProperty.USER_DEFINED:
 306           userDefinedColour.setSelected(true);
 307
 308           break;
 309       }
 310     }
 311
 312   }
 313
 314   private void jbInit()
 315       throws Exception
 316   {
 317     fileMenu.setMnemonic('F');
 318     fileMenu.setText("File");
 319     saveAlignmentMenu.setMnemonic('L');
 320     saveAlignmentMenu.setText("Save As");
 321     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
 322         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
 323     saveAlignmentMenu.addActionListener(new ActionListener()
 324     {
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         saveAlignmentMenu_actionPerformed(e);
 328       }
 329     });
 330     closeMenuItem.setMnemonic('C');
 331     closeMenuItem.setText("Close");
 332     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 333     {
 334       public void actionPerformed(ActionEvent e)
 335       {
 336         closeMenuItem_actionPerformed(e);
 337       }
 338     });
 339     editMenu.setText("Edit");
 340     viewMenu.setText("View");
 341     colourMenu.setText("Colour");
 342     calculateMenu.setText("Calculate");
 343     webService.setText("Web Service");
 344     selectAllSequenceMenuItem.setText("Select all");
 345     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 346         java.awt.event.KeyEvent.VK_A,
 347         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 348     selectAllSequenceMenuItem.addActionListener(new java.awt.event.
 349                                                 ActionListener()
 350     {
 351       public void actionPerformed(ActionEvent e)
 352       {
 353         selectAllSequenceMenuItem_actionPerformed(e);
 354       }
 355     });
 356     deselectAllSequenceMenuItem.setText("Deselect All");
 357     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
 358                                                getKeyStroke(
 359         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 360     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
 361                                                   ActionListener()
 362     {
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         deselectAllSequenceMenuItem_actionPerformed(e);
 366       }
 367     });
 368     invertSequenceMenuItem.setText("Invert Sequence Selection");
 369     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 370     {
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         invertSequenceMenuItem_actionPerformed(e);
 374       }
 375     });
 376     remove2LeftMenuItem.setText("Remove Left");
 377     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 378     {
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         remove2LeftMenuItem_actionPerformed(e);
 382       }
 383     });
 384     remove2RightMenuItem.setText("Remove Right");
 385     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 386     {
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         remove2RightMenuItem_actionPerformed(e);
 390       }
 391     });
 392     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 393     removeGappedColumnMenuItem.addActionListener(new java.awt.event.
 394                                                  ActionListener()
 395     {
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         removeGappedColumnMenuItem_actionPerformed(e);
 399       }
 400     });
 401     removeAllGapsMenuItem.setText("Remove All Gaps");
 402     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 403     {
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         removeAllGapsMenuItem_actionPerformed(e);
 407       }
 408     });
 409     viewBoxesMenuItem.setText("Boxes");
 410     viewBoxesMenuItem.setState(true);
 411     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 412     {
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         viewBoxesMenuItem_actionPerformed(e);
 416       }
 417     });
 418     viewTextMenuItem.setText("Text");
 419     viewTextMenuItem.setState(true);
 420     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 421     {
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         viewTextMenuItem_actionPerformed(e);
 425       }
 426     });
 427     sortPairwiseMenuItem.setText("by Pairwise Identity");
 428     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 429     {
 430       public void actionPerformed(ActionEvent e)
 431       {
 432         sortPairwiseMenuItem_actionPerformed(e);
 433       }
 434     });
 435     sortIDMenuItem.setText("by ID");
 436     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 437     {
 438       public void actionPerformed(ActionEvent e)
 439       {
 440         sortIDMenuItem_actionPerformed(e);
 441       }
 442     });
 443     sortGroupMenuItem.setText("by Group");
 444     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 445     {
 446       public void actionPerformed(ActionEvent e)
 447       {
 448         sortGroupMenuItem_actionPerformed(e);
 449       }
 450     });
 451     removeRedundancyMenuItem.setText("Remove Redundancy...");
 452     removeRedundancyMenuItem.addActionListener(new java.awt.event.
 453                                                ActionListener()
 454     {
 455       public void actionPerformed(ActionEvent e)
 456       {
 457         removeRedundancyMenuItem_actionPerformed(e);
 458       }
 459     });
 460     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 461     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
 462                                                 ActionListener()
 463     {
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         pairwiseAlignmentMenuItem_actionPerformed(e);
 467       }
 468     });
 469     PCAMenuItem.setText("Principal Component Analysis");
 470     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 471     {
 472       public void actionPerformed(ActionEvent e)
 473       {
 474         PCAMenuItem_actionPerformed(e);
 475       }
 476     });
 477     averageDistanceTreeMenuItem.setText(
 478         "Average Distance Using % Identity");
 479     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
 480                                                   ActionListener()
 481     {
 482       public void actionPerformed(ActionEvent e)
 483       {
 484         averageDistanceTreeMenuItem_actionPerformed(e);
 485       }
 486     });
 487     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 488     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 489     {
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         neighbourTreeMenuItem_actionPerformed(e);
 493       }
 494     });
 495     this.getContentPane().setLayout(borderLayout1);
 496     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 497     statusBar.setBackground(Color.white);
 498     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 499     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 500     statusBar.setText("Status bar");
 501     outputTextboxMenu.setMnemonic('T');
 502     outputTextboxMenu.setText("Output to Textbox");
 503     clustalColour.setText("Clustalx");
 504
 505     clustalColour.addActionListener(new java.awt.event.ActionListener()
 506     {
 507       public void actionPerformed(ActionEvent e)
 508       {
 509         clustalColour_actionPerformed(e);
 510       }
 511     });
 512     zappoColour.setText("Zappo");
 513     zappoColour.addActionListener(new java.awt.event.ActionListener()
 514     {
 515       public void actionPerformed(ActionEvent e)
 516       {
 517         zappoColour_actionPerformed(e);
 518       }
 519     });
 520     taylorColour.setText("Taylor");
 521     taylorColour.addActionListener(new java.awt.event.ActionListener()
 522     {
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         taylorColour_actionPerformed(e);
 526       }
 527     });
 528     hydrophobicityColour.setText("Hydrophobicity");
 529     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 530     {
 531       public void actionPerformed(ActionEvent e)
 532       {
 533         hydrophobicityColour_actionPerformed(e);
 534       }
 535     });
 536     helixColour.setText("Helix Propensity");
 537     helixColour.addActionListener(new java.awt.event.ActionListener()
 538     {
 539       public void actionPerformed(ActionEvent e)
 540       {
 541         helixColour_actionPerformed(e);
 542       }
 543     });
 544     strandColour.setText("Strand Propensity");
 545     strandColour.addActionListener(new java.awt.event.ActionListener()
 546     {
 547       public void actionPerformed(ActionEvent e)
 548       {
 549         strandColour_actionPerformed(e);
 550       }
 551     });
 552     turnColour.setText("Turn Propensity");
 553     turnColour.addActionListener(new java.awt.event.ActionListener()
 554     {
 555       public void actionPerformed(ActionEvent e)
 556       {
 557         turnColour_actionPerformed(e);
 558       }
 559     });
 560     buriedColour.setText("Buried Index");
 561     buriedColour.addActionListener(new java.awt.event.ActionListener()
 562     {
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         buriedColour_actionPerformed(e);
 566       }
 567     });
 568     userDefinedColour.setText("User Defined...");
 569     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         userDefinedColour_actionPerformed(e);
 574       }
 575     });
 576     PIDColour.setText("Percentage Identity");
 577     PIDColour.addActionListener(new java.awt.event.ActionListener()
 578     {
 579       public void actionPerformed(ActionEvent e)
 580       {
 581         PIDColour_actionPerformed(e);
 582       }
 583     });
 584     BLOSUM62Colour.setText("BLOSUM62 Score");
 585     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 586     {
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         BLOSUM62Colour_actionPerformed(e);
 590       }
 591     });
 592     avDistanceTreeBlosumMenuItem.setText(
 593         "Average Distance Using BLOSUM62");
 594     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
 595         ActionListener()
 596     {
 597       public void actionPerformed(ActionEvent e)
 598       {
 599         avTreeBlosumMenuItem_actionPerformed(e);
 600       }
 601     });
 602     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 603     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 604     {
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         njTreeBlosumMenuItem_actionPerformed(e);
 608       }
 609     });
 610     annotationPanelMenuItem.setActionCommand("");
 611     annotationPanelMenuItem.setText("Show Annotations");
 612     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
 613     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 614     {
 615       public void actionPerformed(ActionEvent e)
 616       {
 617         annotationPanelMenuItem_actionPerformed(e);
 618       }
 619     });
 620     colourTextMenuItem.setText("Colour Text");
 621     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 622     {
 623       public void actionPerformed(ActionEvent e)
 624       {
 625         colourTextMenuItem_actionPerformed(e);
 626       }
 627     });
 628     htmlMenuItem.setText("HTML");
 629     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 630     {
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         htmlMenuItem_actionPerformed(e);
 634       }
 635     });
 636     overviewMenuItem.setText("Overview Window");
 637     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 638     {
 639       public void actionPerformed(ActionEvent e)
 640       {
 641         overviewMenuItem_actionPerformed(e);
 642       }
 643     });
 644     undoMenuItem.setEnabled(false);
 645     undoMenuItem.setMnemonic('Z');
 646     undoMenuItem.setText("Undo");
 647     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 648         java.awt.event.KeyEvent.VK_Z,
 649         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 650     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 651     {
 652       public void actionPerformed(ActionEvent e)
 653       {
 654         undoMenuItem_actionPerformed(e);
 655       }
 656     });
 657     redoMenuItem.setEnabled(false);
 658     redoMenuItem.setMnemonic('0');
 659     redoMenuItem.setText("Redo");
 660     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 661     {
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         redoMenuItem_actionPerformed(e);
 665       }
 666     });
 667     conservationMenuItem.setText("By Conservation");
 668     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         conservationMenuItem_actionPerformed(e);
 673       }
 674     });
 675     noColourmenuItem.setText("None");
 676     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 677     {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         noColourmenuItem_actionPerformed(e);
 681       }
 682     });
 683     wrapMenuItem.setText("Wrap");
 684     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 685     {
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         wrapMenuItem_actionPerformed(e);
 689       }
 690     });
 691     printMenuItem.setText("Print");
 692     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 693     {
 694       public void actionPerformed(ActionEvent e)
 695       {
 696         printMenuItem_actionPerformed(e);
 697       }
 698     });
 699     renderGapsMenuItem.setText("Show Gaps");
 700     renderGapsMenuItem.setState(true);
 701     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 702     {
 703       public void actionPerformed(ActionEvent e)
 704       {
 705         renderGapsMenuItem_actionPerformed(e);
 706       }
 707     });
 708     findMenuItem.setText("Find...");
 709     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 710         java.awt.event.KeyEvent.VK_F,
 711         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 712     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         findMenuItem_actionPerformed(e);
 717       }
 718     });
 719     searchMenu.setText("Search");
 720
 721     abovePIDThreshold.setText("Above Identity Threshold");
 722     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         abovePIDThreshold_actionPerformed(e);
 727       }
 728     });
 729     showSeqFeatures.setText("Show Sequence Features");
 730     showSeqFeatures.addActionListener(new ActionListener()
 731     {
 732       public void actionPerformed(ActionEvent actionEvent)
 733       {
 734         showSeqFeatures_actionPerformed(actionEvent);
 735       }
 736     });
 737     nucleotideColour.setText("Nucleotide");
 738     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 739     {
 740       public void actionPerformed(ActionEvent e)
 741       {
 742         nucleotideColour_actionPerformed(e);
 743       }
 744     });
 745     deleteGroups.setText("Undefine groups");
 746     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 747     {
 748       public void actionPerformed(ActionEvent e)
 749       {
 750         deleteGroups_actionPerformed(e);
 751       }
 752     });
 753     copy.setText("Copy");
 754     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 755         java.awt.event.KeyEvent.VK_C,
 756         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 757     copy.setMnemonic(KeyEvent.VK_C);
 758
 759     copy.addActionListener(new java.awt.event.ActionListener()
 760     {
 761       public void actionPerformed(ActionEvent e)
 762       {
 763         copy_actionPerformed(e);
 764       }
 765     });
 766     cut.setText("Cut");
 767     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 768         java.awt.event.KeyEvent.VK_X,
 769         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 770     cut.setMnemonic(KeyEvent.VK_X);
 771     cut.addActionListener(new java.awt.event.ActionListener()
 772     {
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         cut_actionPerformed(e);
 776       }
 777     });
 778     delete.setText("Delete");
 779     delete.addActionListener(new java.awt.event.ActionListener()
 780     {
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         delete_actionPerformed(e);
 784       }
 785     });
 786     jMenu1.setMnemonic('V');
 787     jMenu1.setText("Paste");
 788     pasteNew.setText("To New Alignment");
 789     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 790         java.awt.event.KeyEvent.VK_V,
 791         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 792     pasteNew.addActionListener(new java.awt.event.ActionListener()
 793     {
 794       public void actionPerformed(ActionEvent e)
 795       {
 796         pasteNew_actionPerformed(e);
 797       }
 798     });
 799     pasteThis.setText("Add To This Alignment");
 800     pasteThis.addActionListener(new java.awt.event.ActionListener()
 801     {
 802       public void actionPerformed(ActionEvent e)
 803       {
 804         pasteThis_actionPerformed(e);
 805       }
 806     });
 807     applyToAllGroups.setText("Apply Colour To All Groups");
 808     applyToAllGroups.setState(true);
 809     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 810     {
 811       public void actionPerformed(ActionEvent e)
 812       {
 813         applyToAllGroups_actionPerformed(e);
 814       }
 815     });
 816     createPNG.addActionListener(new java.awt.event.ActionListener()
 817     {
 818       public void actionPerformed(ActionEvent e)
 819       {
 820         createPNG(null);
 821       }
 822     });
 823     createPNG.setActionCommand("Save As PNG Image");
 824     createPNG.setText("PNG");
 825     font.setText("Font...");
 826     font.addActionListener(new java.awt.event.ActionListener()
 827     {
 828       public void actionPerformed(ActionEvent e)
 829       {
 830         font_actionPerformed(e);
 831       }
 832     });
 833
 834     seqLimits.setText("Show Sequence Limits");
 835     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
 836     seqLimits.addActionListener(new java.awt.event.ActionListener()
 837     {
 838       public void actionPerformed(ActionEvent e)
 839       {
 840         seqLimit_actionPerformed(e);
 841       }
 842     });
 843     epsFile.setText("EPS");
 844     epsFile.addActionListener(new java.awt.event.ActionListener()
 845     {
 846       public void actionPerformed(ActionEvent e)
 847       {
 848         createEPS(null);
 849       }
 850     });
 851     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 852     LoadtreeMenuItem.setText("Load Associated Tree");
 853     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 854     {
 855       public void actionPerformed(ActionEvent e)
 856       {
 857         LoadtreeMenuItem_actionPerformed(e);
 858       }
 859     });
 860     scaleAbove.setVisible(false);
 861     scaleAbove.setText("Scale Above");
 862     scaleAbove.addActionListener(new java.awt.event.ActionListener()
 863     {
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         scaleAbove_actionPerformed(e);
 867       }
 868     });
 869     scaleLeft.setVisible(false);
 870     scaleLeft.setSelected(true);
 871     scaleLeft.setText("Scale Left");
 872     scaleLeft.addActionListener(new java.awt.event.ActionListener()
 873     {
 874       public void actionPerformed(ActionEvent e)
 875       {
 876         scaleLeft_actionPerformed(e);
 877       }
 878     });
 879     scaleRight.setVisible(false);
 880     scaleRight.setSelected(true);
 881     scaleRight.setText("Scale Right");
 882     scaleRight.addActionListener(new java.awt.event.ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         scaleRight_actionPerformed(e);
 887       }
 888     });
 889     modifyPID.setText("Modify Identity Threshold...");
 890     modifyPID.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         modifyPID_actionPerformed(e);
 895       }
 896     });
 897     modifyConservation.setText("Modify Conservation Threshold...");
 898     modifyConservation.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         modifyConservation_actionPerformed(e);
 903       }
 904     });
 905     sortByTreeMenu.setText("By Tree Order");
 906     sort.setText("Sort");
 907     calculate.setText("Calculate Tree");
 908
 909     jMenu2.setText("Export");
 910     padGapsMenuitem.setText("Pad Gaps");
 911     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
 912     padGapsMenuitem.addActionListener(new ActionListener()
 913     {
 914       public void actionPerformed(ActionEvent e)
 915       {
 916         padGapsMenuitem_actionPerformed(e);
 917       }
 918     });
 919     vamsasStore.setVisible(false);
 920     vamsasStore.setText("VAMSAS store");
 921     vamsasStore.addActionListener(new ActionListener()
 922     {
 923       public void actionPerformed(ActionEvent e)
 924       {
 925         vamsasStore_actionPerformed(e);
 926       }
 927     });
 928     showTranslation.setText("Translate cDNA");
 929     showTranslation.addActionListener(new ActionListener()
 930     {
 931       public void actionPerformed(ActionEvent e)
 932       {
 933         showTranslation_actionPerformed(e);
 934       }
 935     });
 936
 937    /* tabbedPane.addChangeListener(new ChangeListener()
 938         {
 939           public void stateChanged(ChangeEvent ece)
 940           {
 941
 942             tabSelected();
 943           }
 944         });*/
 945     featureSettings.setText("Feature Settings...");
 946     featureSettings.addActionListener(new ActionListener()
 947     {
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         featureSettings_actionPerformed(e);
 951       }
 952     });
 953     fetchSequence.setText("Fetch Sequence(s)...");
 954     fetchSequence.addActionListener(new ActionListener()
 955     {
 956       public void actionPerformed(ActionEvent e)
 957       {
 958         fetchSequence_actionPerformed(e);
 959       }
 960     });
 961     smoothFont.setText("Smooth Fonts");
 962     smoothFont.addActionListener(new ActionListener()
 963     {
 964       public void actionPerformed(ActionEvent e)
 965       {
 966         smoothFont_actionPerformed(e);
 967       }
 968     });
 969     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
 970     annotationColour.setText("By Annotation...");
 971     annotationColour.addActionListener(new ActionListener()
 972     {
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         annotationColour_actionPerformed(e);
 976       }
 977     });
 978     associatedData.setText("Load Features / Annotations");
 979     associatedData.addActionListener(new ActionListener()
 980     {
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         associatedData_actionPerformed(e);
 984       }
 985     });
 986     autoCalculate.setText("Autocalculate Consensus");
 987     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 988     autoCalculate.addActionListener(new ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         autoCalculate_actionPerformed(e);
 993       }
 994     });
 995     addSequenceMenu.setText("Add Sequences");
 996     addFromFile.setText("From File");
 997     addFromFile.addActionListener(new ActionListener()
 998     {
 999       public void actionPerformed(ActionEvent e)
1000       {
1001         addFromFile_actionPerformed(e);
1002       }
1003     });
1004     addFromText.setText("From Textbox");
1005     addFromText.addActionListener(new ActionListener()
1006     {
1007       public void actionPerformed(ActionEvent e)
1008       {
1009         addFromText_actionPerformed(e);
1010       }
1011     });
1012     addFromURL.setText("From URL");
1013     addFromURL.addActionListener(new ActionListener()
1014     {
1015       public void actionPerformed(ActionEvent e)
1016       {
1017         addFromURL_actionPerformed(e);
1018       }
1019     });
1020     exportFeatures.setText("Export Features...");
1021     exportFeatures.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         exportFeatures_actionPerformed(e);
1026       }
1027     });
1028     exportAnnotations.setText("Export Annotations...");
1029     exportAnnotations.addActionListener(new ActionListener()
1030     {
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         exportAnnotations_actionPerformed(e);
1034       }
1035     });
1036     statusPanel.setLayout(gridLayout1);
1037     jMenu3.setText("Show");
1038     showAllSeqs.setText("All Sequences");
1039     showAllSeqs.addActionListener(new ActionListener()
1040     {
1041       public void actionPerformed(ActionEvent e)
1042       {
1043         showAllSeqs_actionPerformed(e);
1044       }
1045     });
1046     showAllColumns.setText("All Columns");
1047     showAllColumns.addActionListener(new ActionListener()
1048     {
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         showAllColumns_actionPerformed(e);
1052       }
1053     });
1054     jMenu4.setText("Hide");
1055     hideSelSequences.setText("Selected Sequences");
1056     hideSelSequences.addActionListener(new ActionListener()
1057     {
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         hideSelSequences_actionPerformed(e);
1061       }
1062     });
1063     hideSelColumns.setText("Selected Columns");
1064     hideSelColumns.addActionListener(new ActionListener()
1065     {
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         hideSelColumns_actionPerformed(e);
1069       }
1070     });
1071     hiddenMarkers.setText("Hidden Markers");
1072     hiddenMarkers.setState(true);
1073     hiddenMarkers.addActionListener(new ActionListener()
1074     {
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         hiddenMarkers_actionPerformed(e);
1078       }
1079     });
1080     invertColSel.setText("Invert Column Selection");
1081     invertColSel.addActionListener(new ActionListener()
1082     {
1083       public void actionPerformed(ActionEvent e)
1084       {
1085         invertColSel_actionPerformed(e);
1086       }
1087     });
1088
1089     alignFrameMenuBar.add(fileMenu);
1090     alignFrameMenuBar.add(editMenu);
1091     alignFrameMenuBar.add(searchMenu);
1092     alignFrameMenuBar.add(viewMenu);
1093     alignFrameMenuBar.add(colourMenu);
1094     alignFrameMenuBar.add(calculateMenu);
1095     alignFrameMenuBar.add(webService);
1096     fileMenu.add(addSequenceMenu);
1097     fileMenu.add(fetchSequence);
1098     fileMenu.addSeparator();
1099     fileMenu.add(vamsasStore);
1100     fileMenu.add(saveAlignmentMenu);
1101     fileMenu.add(jMenu2);
1102     fileMenu.add(outputTextboxMenu);
1103     fileMenu.add(printMenuItem);
1104     fileMenu.addSeparator();
1105     fileMenu.add(exportFeatures);
1106     fileMenu.add(exportAnnotations);
1107     fileMenu.add(LoadtreeMenuItem);
1108     fileMenu.add(associatedData);
1109     fileMenu.addSeparator();
1110     fileMenu.add(closeMenuItem);
1111     editMenu.add(undoMenuItem);
1112     editMenu.add(redoMenuItem);
1113     editMenu.add(cut);
1114     editMenu.add(copy);
1115     editMenu.add(jMenu1);
1116     editMenu.add(delete);
1117     editMenu.addSeparator();
1118     editMenu.add(selectAllSequenceMenuItem);
1119     editMenu.add(deselectAllSequenceMenuItem);
1120     editMenu.add(invertSequenceMenuItem);
1121     editMenu.add(invertColSel);
1122     editMenu.add(deleteGroups);
1123     editMenu.addSeparator();
1124     editMenu.add(remove2LeftMenuItem);
1125     editMenu.add(remove2RightMenuItem);
1126     editMenu.add(removeGappedColumnMenuItem);
1127     editMenu.add(removeAllGapsMenuItem);
1128     editMenu.add(removeRedundancyMenuItem);
1129     editMenu.addSeparator();
1130     editMenu.add(padGapsMenuitem);
1131     searchMenu.add(findMenuItem);
1132     viewMenu.add(font);
1133     viewMenu.add(smoothFont);
1134     viewMenu.addSeparator();
1135     viewMenu.add(jMenu3);
1136     viewMenu.add(jMenu4);
1137     viewMenu.add(hiddenMarkers);
1138     viewMenu.addSeparator();
1139     viewMenu.add(wrapMenuItem);
1140     viewMenu.add(seqLimits);
1141     viewMenu.add(scaleAbove);
1142     viewMenu.add(scaleLeft);
1143     viewMenu.add(scaleRight);
1144     viewMenu.add(viewBoxesMenuItem);
1145     viewMenu.add(viewTextMenuItem);
1146     viewMenu.add(colourTextMenuItem);
1147     viewMenu.add(renderGapsMenuItem);
1148     viewMenu.add(annotationPanelMenuItem);
1149     viewMenu.addSeparator();
1150     viewMenu.add(showSeqFeatures);
1151     viewMenu.add(featureSettings);
1152     viewMenu.addSeparator();
1153     viewMenu.add(overviewMenuItem);
1154     colourMenu.add(applyToAllGroups);
1155     colourMenu.addSeparator();
1156     colourMenu.add(noColourmenuItem);
1157     colourMenu.add(clustalColour);
1158     colourMenu.add(BLOSUM62Colour);
1159     colourMenu.add(PIDColour);
1160     colourMenu.add(zappoColour);
1161     colourMenu.add(taylorColour);
1162     colourMenu.add(hydrophobicityColour);
1163     colourMenu.add(helixColour);
1164     colourMenu.add(strandColour);
1165     colourMenu.add(turnColour);
1166     colourMenu.add(buriedColour);
1167     colourMenu.add(nucleotideColour);
1168     colourMenu.add(userDefinedColour);
1169     colourMenu.addSeparator();
1170     colourMenu.add(conservationMenuItem);
1171     colourMenu.add(modifyConservation);
1172     colourMenu.add(abovePIDThreshold);
1173     colourMenu.add(modifyPID);
1174     colourMenu.add(annotationColour);
1175     calculateMenu.add(sort);
1176     calculateMenu.add(calculate);
1177     calculateMenu.addSeparator();
1178     calculateMenu.add(pairwiseAlignmentMenuItem);
1179     calculateMenu.add(PCAMenuItem);
1180     calculateMenu.addSeparator();
1181     calculateMenu.add(showTranslation);
1182     calculateMenu.add(autoCalculate);
1183     webServiceNoServices=new JMenuItem("<No Services>");
1184     webService.add(webServiceNoServices);jMenu1.add(pasteNew);
1185     jMenu1.add(pasteThis);
1186     sort.add(sortIDMenuItem);
1187     sort.add(sortGroupMenuItem);
1188     sort.add(sortPairwiseMenuItem);
1189     calculate.add(averageDistanceTreeMenuItem);
1190     calculate.add(neighbourTreeMenuItem);
1191     calculate.add(avDistanceTreeBlosumMenuItem);
1192     calculate.add(njTreeBlosumMenuItem);
1193     jMenu2.add(htmlMenuItem);
1194     jMenu2.add(epsFile);
1195     jMenu2.add(createPNG);
1196     addSequenceMenu.add(addFromFile);
1197     addSequenceMenu.add(addFromText);
1198     addSequenceMenu.add(addFromURL);
1199     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1200     statusPanel.add(statusBar, null);
1201     jMenu3.add(showAllColumns);
1202     jMenu3.add(showAllSeqs);
1203     jMenu4.add(hideSelColumns);
1204     jMenu4.add(hideSelSequences);
1205   }
1206
1207   protected void outputText_actionPerformed(ActionEvent e)
1208   {
1209   }
1210
1211   public void addFromFile_actionPerformed(ActionEvent e)
1212   {
1213
1214   }
1215
1216   public void addFromText_actionPerformed(ActionEvent e)
1217   {
1218
1219   }
1220
1221   public void addFromURL_actionPerformed(ActionEvent e)
1222   {
1223
1224   }
1225
1226   public void exportFeatures_actionPerformed(ActionEvent e)
1227   {
1228
1229   }
1230
1231   public void exportAnnotations_actionPerformed(ActionEvent e)
1232   {
1233
1234   }
1235
1236   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1237   {
1238   }
1239
1240   protected void closeMenuItem_actionPerformed(ActionEvent e)
1241   {
1242   }
1243
1244   protected void redoMenuItem_actionPerformed(ActionEvent e)
1245   {
1246   }
1247
1248   protected void undoMenuItem_actionPerformed(ActionEvent e)
1249   {
1250   }
1251
1252   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1253   {
1254   }
1255
1256   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1257   {
1258   }
1259
1260   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1261   {
1262   }
1263
1264   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1265   {
1266   }
1267
1268   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1269   {
1270   }
1271
1272   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1273   {
1274   }
1275
1276   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1277   {
1278   }
1279
1280   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1281   {
1282   }
1283
1284   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1285   {
1286   }
1287
1288   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1289   {
1290   }
1291
1292   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1293   {
1294   }
1295
1296   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1297   {
1298   }
1299
1300   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1301   {
1302   }
1303
1304   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1305   {
1306   }
1307
1308   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1309   {
1310   }
1311
1312   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1313   {
1314   }
1315
1316   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1317   {
1318   }
1319
1320   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1321   {
1322   }
1323
1324   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1325   {
1326   }
1327
1328   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1329   {
1330   }
1331
1332   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1333   {
1334   }
1335
1336   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1337   {
1338   }
1339
1340   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1341   {
1342   }
1343
1344   protected void clustalColour_actionPerformed(ActionEvent e)
1345   {
1346   }
1347
1348   protected void zappoColour_actionPerformed(ActionEvent e)
1349   {
1350   }
1351
1352   protected void taylorColour_actionPerformed(ActionEvent e)
1353   {
1354   }
1355
1356   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1357   {
1358   }
1359
1360   protected void helixColour_actionPerformed(ActionEvent e)
1361   {
1362   }
1363
1364   protected void strandColour_actionPerformed(ActionEvent e)
1365   {
1366   }
1367
1368   protected void turnColour_actionPerformed(ActionEvent e)
1369   {
1370   }
1371
1372   protected void buriedColour_actionPerformed(ActionEvent e)
1373   {
1374   }
1375
1376   protected void userDefinedColour_actionPerformed(ActionEvent e)
1377   {
1378   }
1379
1380   protected void PIDColour_actionPerformed(ActionEvent e)
1381   {
1382   }
1383
1384   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1385   {
1386   }
1387
1388   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1389   {
1390   }
1391
1392   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1393   {
1394   }
1395
1396   protected void printMenuItem_actionPerformed(ActionEvent e)
1397   {
1398   }
1399
1400   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1401   {
1402   }
1403
1404   protected void findMenuItem_actionPerformed(ActionEvent e)
1405   {
1406   }
1407
1408   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1409   {
1410   }
1411
1412   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1413   {
1414   }
1415
1416   protected void nucleotideColour_actionPerformed(ActionEvent e)
1417   {
1418   }
1419
1420   protected void deleteGroups_actionPerformed(ActionEvent e)
1421   {
1422   }
1423
1424   protected void copy_actionPerformed(ActionEvent e)
1425   {
1426   }
1427
1428   protected void cut_actionPerformed(ActionEvent e)
1429   {
1430   }
1431
1432   protected void delete_actionPerformed(ActionEvent e)
1433   {
1434   }
1435
1436   protected void pasteNew_actionPerformed(ActionEvent e)
1437   {
1438   }
1439
1440   protected void pasteThis_actionPerformed(ActionEvent e)
1441   {
1442   }
1443
1444   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1445   {
1446   }
1447
1448   public void createPNG(java.io.File f)
1449   {
1450   }
1451
1452   protected void font_actionPerformed(ActionEvent e)
1453   {
1454   }
1455
1456   protected void seqLimit_actionPerformed(ActionEvent e)
1457   {
1458   }
1459
1460   public void seqDBRef_actionPerformed(ActionEvent e)
1461   {
1462
1463   }
1464
1465
1466   public void createEPS(java.io.File f)
1467   {
1468   }
1469
1470   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1471   {
1472   }
1473
1474   protected void jpred_actionPerformed(ActionEvent e)
1475   {
1476   }
1477
1478   protected void scaleAbove_actionPerformed(ActionEvent e)
1479   {
1480   }
1481
1482   protected void scaleLeft_actionPerformed(ActionEvent e)
1483   {
1484   }
1485
1486   protected void scaleRight_actionPerformed(ActionEvent e)
1487   {
1488   }
1489
1490   protected void modifyPID_actionPerformed(ActionEvent e)
1491   {
1492   }
1493
1494   protected void modifyConservation_actionPerformed(ActionEvent e)
1495   {
1496   }
1497
1498
1499
1500   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
1501   {
1502   }
1503
1504   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1505   {
1506   }
1507
1508
1509   public void vamsasStore_actionPerformed(ActionEvent e)
1510   {
1511
1512   }
1513
1514   public void vamsasLoad_actionPerformed(ActionEvent e)
1515   {
1516
1517   }
1518
1519   public void showTranslation_actionPerformed(ActionEvent e)
1520   {
1521
1522   }
1523
1524   public void featureSettings_actionPerformed(ActionEvent e)
1525   {
1526
1527   }
1528
1529   public void fetchSequence_actionPerformed(ActionEvent e)
1530   {
1531
1532   }
1533
1534   public void smoothFont_actionPerformed(ActionEvent e)
1535   {
1536
1537   }
1538
1539   public void annotationColour_actionPerformed(ActionEvent e)
1540   {
1541
1542   }
1543
1544
1545   public void associatedData_actionPerformed(ActionEvent e)
1546   {
1547
1548   }
1549
1550   public void autoCalculate_actionPerformed(ActionEvent e)
1551   {
1552
1553   }
1554
1555   public void showAllSeqs_actionPerformed(ActionEvent e)
1556   {
1557
1558   }
1559
1560   public void showAllColumns_actionPerformed(ActionEvent e)
1561   {
1562
1563   }
1564
1565   public void hideSelSequences_actionPerformed(ActionEvent e)
1566   {
1567
1568   }
1569
1570   public void hideSelColumns_actionPerformed(ActionEvent e)
1571   {
1572
1573   }
1574
1575   public void hiddenMarkers_actionPerformed(ActionEvent e)
1576   {
1577
1578   }
1579
1580   public void findPdbId_actionPerformed(ActionEvent e)
1581   {
1582
1583   }
1584
1585   public void enterPdbId_actionPerformed(ActionEvent e)
1586   {
1587
1588   }
1589
1590   public void pdbFile_actionPerformed(ActionEvent e)
1591   {
1592
1593   }
1594
1595   public void invertColSel_actionPerformed(ActionEvent e)
1596   {
1597
1598   }
1599 }