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