src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.jbgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 \r
  26 import jalview.schemes.*;\r
  27 import java.awt.BorderLayout;\r
  28 \r
  29 \r
  30 \r
  31 \r
  32 public class GAlignFrame\r
  33     extends JInternalFrame\r
  34 {\r
  35   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  36   protected JMenu fileMenu = new JMenu();\r
  37   protected JMenuItem closeMenuItem = new JMenuItem();\r
  38   protected JMenu editMenu = new JMenu();\r
  39   protected JMenu viewMenu = new JMenu();\r
  40   protected JMenu colourMenu = new JMenu();\r
  41   protected JMenu calculateMenu = new JMenu();\r
  42   protected JMenu webService = new JMenu();\r
  43   protected JMenuItem webServiceNoServices;\r
  44   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  45   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  46   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  47   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  48   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  50   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  51   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  52   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  53   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  54   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  55   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  56   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  57   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  58   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  59   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  60   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  61   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  62   BorderLayout borderLayout1 = new BorderLayout();\r
  63   public JLabel statusBar = new JLabel();\r
  64   protected JMenuItem saveAs = new JMenuItem();\r
  65   protected JMenu outputTextboxMenu = new JMenu();\r
  66   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  70       JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  75   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  76   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  77   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  78   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  79   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  80   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  81   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  82   JMenuItem htmlMenuItem = new JMenuItem();\r
  83   JMenuItem overviewMenuItem = new JMenuItem();\r
  84   protected JMenuItem undoMenuItem = new JMenuItem();\r
  85   protected JMenuItem redoMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  87   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  88   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  89   JMenuItem printMenuItem = new JMenuItem();\r
  90   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  91   JMenuItem findMenuItem = new JMenuItem();\r
  92   JMenu searchMenu = new JMenu();\r
  93   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  94   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  95   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  96   JMenuItem deleteGroups = new JMenuItem();\r
  97   JMenuItem delete = new JMenuItem();\r
  98   JMenuItem copy = new JMenuItem();\r
  99   JMenuItem cut = new JMenuItem();\r
 100   JMenu jMenu1 = new JMenu();\r
 101   JMenuItem pasteNew = new JMenuItem();\r
 102   JMenuItem pasteThis = new JMenuItem();\r
 103   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 104   JMenuItem createPNG = new JMenuItem();\r
 105   protected JMenuItem font = new JMenuItem();\r
 106   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 107   JMenuItem epsFile = new JMenuItem();\r
 108   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 109   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 110   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 111   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 112   protected JMenuItem modifyPID = new JMenuItem();\r
 113   protected JMenuItem modifyConservation = new JMenuItem();\r
 114   protected JMenu sortByTreeMenu = new JMenu();\r
 115   protected JMenu sort = new JMenu();\r
 116   JMenu calculate = new JMenu();\r
 117   JMenu jMenu2 = new JMenu();\r
 118   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 119   protected ButtonGroup colours = new ButtonGroup();\r
 120   JMenuItem vamsasStore = new JMenuItem();\r
 121   protected JMenuItem showTranslation = new JMenuItem();\r
 122   public JMenuItem featureSettings = new JMenuItem();\r
 123   JMenuItem fetchSequence = new JMenuItem();\r
 124   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 125   JMenuItem annotationColour = new JMenuItem();\r
 126   JMenuItem associatedData = new JMenuItem();\r
 127   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 128   JMenu addSequenceMenu = new JMenu();\r
 129   JMenuItem addFromFile = new JMenuItem();\r
 130   JMenuItem addFromText = new JMenuItem();\r
 131   JMenuItem addFromURL = new JMenuItem();\r
 132   JMenuItem exportAnnotations = new JMenuItem();\r
 133   JMenuItem exportFeatures = new JMenuItem();\r
 134   protected JPanel statusPanel = new JPanel();\r
 135   GridLayout gridLayout1 = new GridLayout();\r
 136   JMenu jMenu3 = new JMenu();\r
 137   JMenuItem showAllSeqs = new JMenuItem();\r
 138   JMenuItem showAllColumns = new JMenuItem();\r
 139   JMenu hideMenu = new JMenu();\r
 140   JMenuItem hideSelSequences = new JMenuItem();\r
 141   JMenuItem hideSelColumns = new JMenuItem();\r
 142   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 143   JMenuItem invertColSel = new JMenuItem();\r
 144   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 145   JMenuItem save = new JMenuItem();\r
 146   public GAlignFrame()\r
 147   {\r
 148     try\r
 149     {\r
 150       jbInit();\r
 151       setJMenuBar(alignFrameMenuBar);\r
 152 \r
 153       // dynamically fill save as menu with available formats\r
 154       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 155       {\r
 156         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 157 \r
 158         item.addActionListener(new java.awt.event.ActionListener()\r
 159         {\r
 160           public void actionPerformed(ActionEvent e)\r
 161           {\r
 162             outputText_actionPerformed(e);\r
 163           }\r
 164         });\r
 165 \r
 166         outputTextboxMenu.add(item);\r
 167       }\r
 168     }\r
 169     catch (Exception e)\r
 170     {\r
 171     }\r
 172 \r
 173 \r
 174     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 175     {\r
 176       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 177           getUserColourSchemes().keys();\r
 178 \r
 179       while (userColours.hasMoreElements())\r
 180       {\r
 181         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 182             nextElement().toString());\r
 183         radioItem.setName("USER_DEFINED");\r
 184         radioItem.addMouseListener(new MouseAdapter()\r
 185             {\r
 186               public void mousePressed(MouseEvent evt)\r
 187               {\r
 188                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 189                 {\r
 190                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 191 \r
 192                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 193                       "Remove from default list?",\r
 194                       "Remove user defined colour",\r
 195                       JOptionPane.YES_NO_OPTION);\r
 196                   if(option == JOptionPane.YES_OPTION)\r
 197                   {\r
 198                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 199                     colourMenu.remove(radioItem);\r
 200                   }\r
 201                   else\r
 202                     radioItem.addActionListener(new ActionListener()\r
 203                     {\r
 204                       public void actionPerformed(ActionEvent evt)\r
 205                       {\r
 206                         userDefinedColour_actionPerformed(evt);\r
 207                       }\r
 208                     });\r
 209                 }\r
 210               }\r
 211             });\r
 212         radioItem.addActionListener(new ActionListener()\r
 213         {\r
 214           public void actionPerformed(ActionEvent evt)\r
 215           {\r
 216             userDefinedColour_actionPerformed(evt);\r
 217           }\r
 218         });\r
 219         colourMenu.insert(radioItem, 15);\r
 220         colours.add(radioItem);\r
 221       }\r
 222     }\r
 223     colours.add(noColourmenuItem);\r
 224     colours.add(clustalColour);\r
 225     colours.add(zappoColour);\r
 226     colours.add(taylorColour);\r
 227     colours.add(hydrophobicityColour);\r
 228     colours.add(helixColour);\r
 229     colours.add(strandColour);\r
 230     colours.add(turnColour);\r
 231     colours.add(buriedColour);\r
 232     colours.add(userDefinedColour);\r
 233     colours.add(PIDColour);\r
 234     colours.add(BLOSUM62Colour);\r
 235     colours.add(nucleotideColour);\r
 236 \r
 237     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 238 \r
 239 \r
 240   }\r
 241 \r
 242   public void setColourSelected(String defaultColour)\r
 243   {\r
 244 \r
 245     if (defaultColour != null)\r
 246     {\r
 247       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 248 \r
 249       switch (index)\r
 250       {\r
 251         case ColourSchemeProperty.NONE:\r
 252               noColourmenuItem.setSelected(true);\r
 253               break;\r
 254         case ColourSchemeProperty.CLUSTAL:\r
 255           clustalColour.setSelected(true);\r
 256 \r
 257           break;\r
 258 \r
 259         case ColourSchemeProperty.BLOSUM:\r
 260           BLOSUM62Colour.setSelected(true);\r
 261 \r
 262           break;\r
 263 \r
 264         case ColourSchemeProperty.PID:\r
 265           PIDColour.setSelected(true);\r
 266 \r
 267           break;\r
 268 \r
 269         case ColourSchemeProperty.ZAPPO:\r
 270           zappoColour.setSelected(true);\r
 271 \r
 272           break;\r
 273 \r
 274         case ColourSchemeProperty.TAYLOR:\r
 275           taylorColour.setSelected(true);\r
 276           break;\r
 277 \r
 278         case ColourSchemeProperty.HYDROPHOBIC:\r
 279           hydrophobicityColour.setSelected(true);\r
 280 \r
 281           break;\r
 282 \r
 283         case ColourSchemeProperty.HELIX:\r
 284           helixColour.setSelected(true);\r
 285 \r
 286           break;\r
 287 \r
 288         case ColourSchemeProperty.STRAND:\r
 289           strandColour.setSelected(true);\r
 290 \r
 291           break;\r
 292 \r
 293         case ColourSchemeProperty.TURN:\r
 294           turnColour.setSelected(true);\r
 295 \r
 296           break;\r
 297 \r
 298         case ColourSchemeProperty.BURIED:\r
 299           buriedColour.setSelected(true);\r
 300 \r
 301           break;\r
 302 \r
 303         case ColourSchemeProperty.NUCLEOTIDE:\r
 304           nucleotideColour.setSelected(true);\r
 305 \r
 306           break;\r
 307 \r
 308         case ColourSchemeProperty.USER_DEFINED:\r
 309           userDefinedColour.setSelected(true);\r
 310 \r
 311           break;\r
 312       }\r
 313     }\r
 314 \r
 315   }\r
 316 \r
 317   private void jbInit()\r
 318       throws Exception\r
 319   {\r
 320     fileMenu.setText("File");\r
 321     saveAs.setText("Save As ...");\r
 322     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 323         KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));\r
 324     saveAs.addActionListener(new ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         saveAs_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     closeMenuItem.setMnemonic('C');\r
 332     closeMenuItem.setText("Close");\r
 333     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 334         event.KeyEvent.VK_W, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 335     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 336     {\r
 337       public void actionPerformed(ActionEvent e)\r
 338       {\r
 339         closeMenuItem_actionPerformed(e);\r
 340       }\r
 341     });\r
 342     editMenu.setText("Edit");\r
 343     viewMenu.setText("View");\r
 344     colourMenu.setText("Colour");\r
 345     calculateMenu.setText("Calculate");\r
 346     webService.setText("Web Service");\r
 347     selectAllSequenceMenuItem.setText("Select all");\r
 348     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 349         java.awt.event.KeyEvent.VK_A,\r
 350         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 351     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 352                                                 ActionListener()\r
 353     {\r
 354       public void actionPerformed(ActionEvent e)\r
 355       {\r
 356         selectAllSequenceMenuItem_actionPerformed(e);\r
 357       }\r
 358     });\r
 359     deselectAllSequenceMenuItem.setText("Deselect All");\r
 360     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 361                                                getKeyStroke(\r
 362         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 363     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 364                                                   ActionListener()\r
 365     {\r
 366       public void actionPerformed(ActionEvent e)\r
 367       {\r
 368         deselectAllSequenceMenuItem_actionPerformed(e);\r
 369       }\r
 370     });\r
 371     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 372     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 373         java.awt.event.KeyEvent.VK_I,\r
 374         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 375     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 376     {\r
 377       public void actionPerformed(ActionEvent e)\r
 378       {\r
 379         invertSequenceMenuItem_actionPerformed(e);\r
 380       }\r
 381     });\r
 382     remove2LeftMenuItem.setText("Remove Left");\r
 383     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 384         awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 385     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 386     {\r
 387       public void actionPerformed(ActionEvent e)\r
 388       {\r
 389         remove2LeftMenuItem_actionPerformed(e);\r
 390       }\r
 391     });\r
 392     remove2RightMenuItem.setText("Remove Right");\r
 393     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 394         awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 395     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         remove2RightMenuItem_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 403     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 404                                               getKeyStroke(java.awt.event.\r
 405         KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 406     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 407                                                  ActionListener()\r
 408     {\r
 409       public void actionPerformed(ActionEvent e)\r
 410       {\r
 411         removeGappedColumnMenuItem_actionPerformed(e);\r
 412       }\r
 413     });\r
 414     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 415     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 416         java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 417     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 418     {\r
 419       public void actionPerformed(ActionEvent e)\r
 420       {\r
 421         removeAllGapsMenuItem_actionPerformed(e);\r
 422       }\r
 423     });\r
 424     viewBoxesMenuItem.setText("Boxes");\r
 425     viewBoxesMenuItem.setState(true);\r
 426     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 427     {\r
 428       public void actionPerformed(ActionEvent e)\r
 429       {\r
 430         viewBoxesMenuItem_actionPerformed(e);\r
 431       }\r
 432     });\r
 433     viewTextMenuItem.setText("Text");\r
 434     viewTextMenuItem.setState(true);\r
 435     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         viewTextMenuItem_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 443     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 444     {\r
 445       public void actionPerformed(ActionEvent e)\r
 446       {\r
 447         sortPairwiseMenuItem_actionPerformed(e);\r
 448       }\r
 449     });\r
 450     sortIDMenuItem.setText("by ID");\r
 451     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 452     {\r
 453       public void actionPerformed(ActionEvent e)\r
 454       {\r
 455         sortIDMenuItem_actionPerformed(e);\r
 456       }\r
 457     });\r
 458     sortGroupMenuItem.setText("by Group");\r
 459     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 460     {\r
 461       public void actionPerformed(ActionEvent e)\r
 462       {\r
 463         sortGroupMenuItem_actionPerformed(e);\r
 464       }\r
 465     });\r
 466     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 467     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 468         java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 469     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 470                                                ActionListener()\r
 471     {\r
 472       public void actionPerformed(ActionEvent e)\r
 473       {\r
 474         removeRedundancyMenuItem_actionPerformed(e);\r
 475       }\r
 476     });\r
 477     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 478     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 479                                                 ActionListener()\r
 480     {\r
 481       public void actionPerformed(ActionEvent e)\r
 482       {\r
 483         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 484       }\r
 485     });\r
 486     PCAMenuItem.setText("Principal Component Analysis");\r
 487     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 488     {\r
 489       public void actionPerformed(ActionEvent e)\r
 490       {\r
 491         PCAMenuItem_actionPerformed(e);\r
 492       }\r
 493     });\r
 494     averageDistanceTreeMenuItem.setText(\r
 495         "Average Distance Using % Identity");\r
 496     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 497                                                   ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         averageDistanceTreeMenuItem_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 505     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         neighbourTreeMenuItem_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     this.getContentPane().setLayout(borderLayout1);\r
 513     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 514     statusBar.setBackground(Color.white);\r
 515     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 516     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 517     statusBar.setText("Status bar");\r
 518     outputTextboxMenu.setMnemonic('T');\r
 519     outputTextboxMenu.setText("Output to Textbox");\r
 520     clustalColour.setText("Clustalx");\r
 521 \r
 522     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         clustalColour_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     zappoColour.setText("Zappo");\r
 530     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         zappoColour_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     taylorColour.setText("Taylor");\r
 538     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 539     {\r
 540       public void actionPerformed(ActionEvent e)\r
 541       {\r
 542         taylorColour_actionPerformed(e);\r
 543       }\r
 544     });\r
 545     hydrophobicityColour.setText("Hydrophobicity");\r
 546     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         hydrophobicityColour_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     helixColour.setText("Helix Propensity");\r
 554     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         helixColour_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     strandColour.setText("Strand Propensity");\r
 562     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 563     {\r
 564       public void actionPerformed(ActionEvent e)\r
 565       {\r
 566         strandColour_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     turnColour.setText("Turn Propensity");\r
 570     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent e)\r
 573       {\r
 574         turnColour_actionPerformed(e);\r
 575       }\r
 576     });\r
 577     buriedColour.setText("Buried Index");\r
 578     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent e)\r
 581       {\r
 582         buriedColour_actionPerformed(e);\r
 583       }\r
 584     });\r
 585     userDefinedColour.setText("User Defined...");\r
 586     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 587     {\r
 588       public void actionPerformed(ActionEvent e)\r
 589       {\r
 590         userDefinedColour_actionPerformed(e);\r
 591       }\r
 592     });\r
 593     PIDColour.setText("Percentage Identity");\r
 594     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 595     {\r
 596       public void actionPerformed(ActionEvent e)\r
 597       {\r
 598         PIDColour_actionPerformed(e);\r
 599       }\r
 600     });\r
 601     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 602     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 603     {\r
 604       public void actionPerformed(ActionEvent e)\r
 605       {\r
 606         BLOSUM62Colour_actionPerformed(e);\r
 607       }\r
 608     });\r
 609     avDistanceTreeBlosumMenuItem.setText(\r
 610         "Average Distance Using BLOSUM62");\r
 611     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 612         ActionListener()\r
 613     {\r
 614       public void actionPerformed(ActionEvent e)\r
 615       {\r
 616         avTreeBlosumMenuItem_actionPerformed(e);\r
 617       }\r
 618     });\r
 619     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 620     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 621     {\r
 622       public void actionPerformed(ActionEvent e)\r
 623       {\r
 624         njTreeBlosumMenuItem_actionPerformed(e);\r
 625       }\r
 626     });\r
 627     annotationPanelMenuItem.setActionCommand("");\r
 628     annotationPanelMenuItem.setText("Show Annotations");\r
 629     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 630     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 631     {\r
 632       public void actionPerformed(ActionEvent e)\r
 633       {\r
 634         annotationPanelMenuItem_actionPerformed(e);\r
 635       }\r
 636     });\r
 637     colourTextMenuItem.setText("Colour Text");\r
 638     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 639     {\r
 640       public void actionPerformed(ActionEvent e)\r
 641       {\r
 642         colourTextMenuItem_actionPerformed(e);\r
 643       }\r
 644     });\r
 645     htmlMenuItem.setText("HTML");\r
 646     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 647     {\r
 648       public void actionPerformed(ActionEvent e)\r
 649       {\r
 650         htmlMenuItem_actionPerformed(e);\r
 651       }\r
 652     });\r
 653     overviewMenuItem.setText("Overview Window");\r
 654     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 655     {\r
 656       public void actionPerformed(ActionEvent e)\r
 657       {\r
 658         overviewMenuItem_actionPerformed(e);\r
 659       }\r
 660     });\r
 661     undoMenuItem.setEnabled(false);\r
 662     undoMenuItem.setMnemonic('Z');\r
 663     undoMenuItem.setText("Undo");\r
 664     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 665         java.awt.event.KeyEvent.VK_Z,\r
 666         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 667     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 668     {\r
 669       public void actionPerformed(ActionEvent e)\r
 670       {\r
 671         undoMenuItem_actionPerformed(e);\r
 672       }\r
 673     });\r
 674     redoMenuItem.setEnabled(false);\r
 675     redoMenuItem.setMnemonic('0');\r
 676     redoMenuItem.setText("Redo");\r
 677     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 678         event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 679     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 680     {\r
 681       public void actionPerformed(ActionEvent e)\r
 682       {\r
 683         redoMenuItem_actionPerformed(e);\r
 684       }\r
 685     });\r
 686     conservationMenuItem.setText("By Conservation");\r
 687     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 688     {\r
 689       public void actionPerformed(ActionEvent e)\r
 690       {\r
 691         conservationMenuItem_actionPerformed(e);\r
 692       }\r
 693     });\r
 694     noColourmenuItem.setText("None");\r
 695     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 696     {\r
 697       public void actionPerformed(ActionEvent e)\r
 698       {\r
 699         noColourmenuItem_actionPerformed(e);\r
 700       }\r
 701     });\r
 702     wrapMenuItem.setText("Wrap");\r
 703     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 704     {\r
 705       public void actionPerformed(ActionEvent e)\r
 706       {\r
 707         wrapMenuItem_actionPerformed(e);\r
 708       }\r
 709     });\r
 710     printMenuItem.setText("Print");\r
 711     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 712         event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 713     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 714     {\r
 715       public void actionPerformed(ActionEvent e)\r
 716       {\r
 717         printMenuItem_actionPerformed(e);\r
 718       }\r
 719     });\r
 720     renderGapsMenuItem.setText("Show Gaps");\r
 721     renderGapsMenuItem.setState(true);\r
 722     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 723     {\r
 724       public void actionPerformed(ActionEvent e)\r
 725       {\r
 726         renderGapsMenuItem_actionPerformed(e);\r
 727       }\r
 728     });\r
 729     findMenuItem.setText("Find...");\r
 730     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 731         java.awt.event.KeyEvent.VK_F,\r
 732         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 733     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 734     {\r
 735       public void actionPerformed(ActionEvent e)\r
 736       {\r
 737         findMenuItem_actionPerformed(e);\r
 738       }\r
 739     });\r
 740     searchMenu.setText("Search");\r
 741 \r
 742     abovePIDThreshold.setText("Above Identity Threshold");\r
 743     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 744     {\r
 745       public void actionPerformed(ActionEvent e)\r
 746       {\r
 747         abovePIDThreshold_actionPerformed(e);\r
 748       }\r
 749     });\r
 750     showSeqFeatures.setText("Show Sequence Features");\r
 751     showSeqFeatures.addActionListener(new ActionListener()\r
 752     {\r
 753       public void actionPerformed(ActionEvent actionEvent)\r
 754       {\r
 755         showSeqFeatures_actionPerformed(actionEvent);\r
 756       }\r
 757     });\r
 758     nucleotideColour.setText("Nucleotide");\r
 759     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 760     {\r
 761       public void actionPerformed(ActionEvent e)\r
 762       {\r
 763         nucleotideColour_actionPerformed(e);\r
 764       }\r
 765     });\r
 766     deleteGroups.setText("Undefine groups");\r
 767     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 768         event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 769     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 770     {\r
 771       public void actionPerformed(ActionEvent e)\r
 772       {\r
 773         deleteGroups_actionPerformed(e);\r
 774       }\r
 775     });\r
 776     copy.setText("Copy");\r
 777     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 778         java.awt.event.KeyEvent.VK_C,\r
 779         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 780     copy.setMnemonic(KeyEvent.VK_C);\r
 781 \r
 782     copy.addActionListener(new java.awt.event.ActionListener()\r
 783     {\r
 784       public void actionPerformed(ActionEvent e)\r
 785       {\r
 786         copy_actionPerformed(e);\r
 787       }\r
 788     });\r
 789     cut.setText("Cut");\r
 790     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 791         java.awt.event.KeyEvent.VK_X,\r
 792         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 793     cut.setMnemonic(KeyEvent.VK_X);\r
 794     cut.addActionListener(new java.awt.event.ActionListener()\r
 795     {\r
 796       public void actionPerformed(ActionEvent e)\r
 797       {\r
 798         cut_actionPerformed(e);\r
 799       }\r
 800     });\r
 801     delete.setText("Delete");\r
 802     delete.addActionListener(new java.awt.event.ActionListener()\r
 803     {\r
 804       public void actionPerformed(ActionEvent e)\r
 805       {\r
 806         delete_actionPerformed(e);\r
 807       }\r
 808     });\r
 809     jMenu1.setMnemonic('V');\r
 810     jMenu1.setText("Paste");\r
 811     pasteNew.setText("To New Alignment");\r
 812     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 813         java.awt.event.KeyEvent.VK_V,\r
 814         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 815     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 816     {\r
 817       public void actionPerformed(ActionEvent e)\r
 818       {\r
 819         pasteNew_actionPerformed(e);\r
 820       }\r
 821     });\r
 822     pasteThis.setText("Add To This Alignment");\r
 823     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 824     {\r
 825       public void actionPerformed(ActionEvent e)\r
 826       {\r
 827         pasteThis_actionPerformed(e);\r
 828       }\r
 829     });\r
 830     applyToAllGroups.setText("Apply Colour To All Groups");\r
 831     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 832     {\r
 833       public void actionPerformed(ActionEvent e)\r
 834       {\r
 835         applyToAllGroups_actionPerformed(e);\r
 836       }\r
 837     });\r
 838     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 839     {\r
 840       public void actionPerformed(ActionEvent e)\r
 841       {\r
 842         createPNG(null);\r
 843       }\r
 844     });\r
 845     createPNG.setActionCommand("Save As PNG Image");\r
 846     createPNG.setText("PNG");\r
 847     font.setText("Font...");\r
 848     font.addActionListener(new java.awt.event.ActionListener()\r
 849     {\r
 850       public void actionPerformed(ActionEvent e)\r
 851       {\r
 852         font_actionPerformed(e);\r
 853       }\r
 854     });\r
 855 \r
 856     seqLimits.setText("Show Sequence Limits");\r
 857     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 858     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 859     {\r
 860       public void actionPerformed(ActionEvent e)\r
 861       {\r
 862         seqLimit_actionPerformed(e);\r
 863       }\r
 864     });\r
 865     epsFile.setText("EPS");\r
 866     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 867     {\r
 868       public void actionPerformed(ActionEvent e)\r
 869       {\r
 870         createEPS(null);\r
 871       }\r
 872     });\r
 873     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 874     LoadtreeMenuItem.setText("Load Associated Tree");\r
 875     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 876     {\r
 877       public void actionPerformed(ActionEvent e)\r
 878       {\r
 879         LoadtreeMenuItem_actionPerformed(e);\r
 880       }\r
 881     });\r
 882     scaleAbove.setVisible(false);\r
 883     scaleAbove.setText("Scale Above");\r
 884     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 885     {\r
 886       public void actionPerformed(ActionEvent e)\r
 887       {\r
 888         scaleAbove_actionPerformed(e);\r
 889       }\r
 890     });\r
 891     scaleLeft.setVisible(false);\r
 892     scaleLeft.setSelected(true);\r
 893     scaleLeft.setText("Scale Left");\r
 894     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 895     {\r
 896       public void actionPerformed(ActionEvent e)\r
 897       {\r
 898         scaleLeft_actionPerformed(e);\r
 899       }\r
 900     });\r
 901     scaleRight.setVisible(false);\r
 902     scaleRight.setSelected(true);\r
 903     scaleRight.setText("Scale Right");\r
 904     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 905     {\r
 906       public void actionPerformed(ActionEvent e)\r
 907       {\r
 908         scaleRight_actionPerformed(e);\r
 909       }\r
 910     });\r
 911     modifyPID.setText("Modify Identity Threshold...");\r
 912     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 913     {\r
 914       public void actionPerformed(ActionEvent e)\r
 915       {\r
 916         modifyPID_actionPerformed(e);\r
 917       }\r
 918     });\r
 919     modifyConservation.setText("Modify Conservation Threshold...");\r
 920     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 921     {\r
 922       public void actionPerformed(ActionEvent e)\r
 923       {\r
 924         modifyConservation_actionPerformed(e);\r
 925       }\r
 926     });\r
 927     sortByTreeMenu.setText("By Tree Order");\r
 928     sort.setText("Sort");\r
 929     calculate.setText("Calculate Tree");\r
 930 \r
 931     jMenu2.setText("Export Image");\r
 932     padGapsMenuitem.setText("Pad Gaps");\r
 933     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 934     padGapsMenuitem.addActionListener(new ActionListener()\r
 935     {\r
 936       public void actionPerformed(ActionEvent e)\r
 937       {\r
 938         padGapsMenuitem_actionPerformed(e);\r
 939       }\r
 940     });\r
 941     vamsasStore.setVisible(false);\r
 942     vamsasStore.setText("VAMSAS store");\r
 943     vamsasStore.addActionListener(new ActionListener()\r
 944     {\r
 945       public void actionPerformed(ActionEvent e)\r
 946       {\r
 947         vamsasStore_actionPerformed(e);\r
 948       }\r
 949     });\r
 950     showTranslation.setText("Translate cDNA");\r
 951     showTranslation.addActionListener(new ActionListener()\r
 952     {\r
 953       public void actionPerformed(ActionEvent e)\r
 954       {\r
 955         showTranslation_actionPerformed(e);\r
 956       }\r
 957     });\r
 958 \r
 959 \r
 960     featureSettings.setText("Feature Settings...");\r
 961     featureSettings.addActionListener(new ActionListener()\r
 962     {\r
 963       public void actionPerformed(ActionEvent e)\r
 964       {\r
 965         featureSettings_actionPerformed(e);\r
 966       }\r
 967     });\r
 968     fetchSequence.setText("Fetch Sequence(s)...");\r
 969     fetchSequence.addActionListener(new ActionListener()\r
 970     {\r
 971       public void actionPerformed(ActionEvent e)\r
 972       {\r
 973         fetchSequence_actionPerformed(e);\r
 974       }\r
 975     });\r
 976     smoothFont.setText("Smooth Fonts");\r
 977     smoothFont.addActionListener(new ActionListener()\r
 978     {\r
 979       public void actionPerformed(ActionEvent e)\r
 980       {\r
 981         smoothFont_actionPerformed(e);\r
 982       }\r
 983     });\r
 984 \r
 985     annotationColour.setText("By Annotation...");\r
 986     annotationColour.addActionListener(new ActionListener()\r
 987     {\r
 988       public void actionPerformed(ActionEvent e)\r
 989       {\r
 990         annotationColour_actionPerformed(e);\r
 991       }\r
 992     });\r
 993     associatedData.setText("Load Features / Annotations");\r
 994     associatedData.addActionListener(new ActionListener()\r
 995     {\r
 996       public void actionPerformed(ActionEvent e)\r
 997       {\r
 998         associatedData_actionPerformed(e);\r
 999       }\r
1000     });\r
1001     autoCalculate.setText("Autocalculate Consensus");\r
1002     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1003     autoCalculate.addActionListener(new ActionListener()\r
1004     {\r
1005       public void actionPerformed(ActionEvent e)\r
1006       {\r
1007         autoCalculate_actionPerformed(e);\r
1008       }\r
1009     });\r
1010     addSequenceMenu.setText("Add Sequences");\r
1011     addFromFile.setText("From File");\r
1012     addFromFile.addActionListener(new ActionListener()\r
1013     {\r
1014       public void actionPerformed(ActionEvent e)\r
1015       {\r
1016         addFromFile_actionPerformed(e);\r
1017       }\r
1018     });\r
1019     addFromText.setText("From Textbox");\r
1020     addFromText.addActionListener(new ActionListener()\r
1021     {\r
1022       public void actionPerformed(ActionEvent e)\r
1023       {\r
1024         addFromText_actionPerformed(e);\r
1025       }\r
1026     });\r
1027     addFromURL.setText("From URL");\r
1028     addFromURL.addActionListener(new ActionListener()\r
1029     {\r
1030       public void actionPerformed(ActionEvent e)\r
1031       {\r
1032         addFromURL_actionPerformed(e);\r
1033       }\r
1034     });\r
1035     exportFeatures.setText("Export Features...");\r
1036     exportFeatures.addActionListener(new ActionListener()\r
1037     {\r
1038       public void actionPerformed(ActionEvent e)\r
1039       {\r
1040         exportFeatures_actionPerformed(e);\r
1041       }\r
1042     });\r
1043     exportAnnotations.setText("Export Annotations...");\r
1044     exportAnnotations.addActionListener(new ActionListener()\r
1045     {\r
1046       public void actionPerformed(ActionEvent e)\r
1047       {\r
1048         exportAnnotations_actionPerformed(e);\r
1049       }\r
1050     });\r
1051     statusPanel.setLayout(gridLayout1);\r
1052     jMenu3.setText("Show");\r
1053     showAllSeqs.setText("All Sequences");\r
1054     showAllSeqs.addActionListener(new ActionListener()\r
1055     {\r
1056       public void actionPerformed(ActionEvent e)\r
1057       {\r
1058         showAllSeqs_actionPerformed(e);\r
1059       }\r
1060     });\r
1061     showAllColumns.setText("All Columns");\r
1062     showAllColumns.addActionListener(new ActionListener()\r
1063     {\r
1064       public void actionPerformed(ActionEvent e)\r
1065       {\r
1066         showAllColumns_actionPerformed(e);\r
1067       }\r
1068     });\r
1069     hideMenu.setText("Hide");\r
1070     hideSelSequences.setText("Selected Sequences");\r
1071     hideSelSequences.addActionListener(new ActionListener()\r
1072     {\r
1073       public void actionPerformed(ActionEvent e)\r
1074       {\r
1075         hideSelSequences_actionPerformed(e);\r
1076       }\r
1077     });\r
1078     hideSelColumns.setText("Selected Columns");\r
1079     hideSelColumns.addActionListener(new ActionListener()\r
1080     {\r
1081       public void actionPerformed(ActionEvent e)\r
1082       {\r
1083         hideSelColumns_actionPerformed(e);\r
1084       }\r
1085     });\r
1086     hiddenMarkers.setText("Hidden Markers");\r
1087     hiddenMarkers.addActionListener(new ActionListener()\r
1088     {\r
1089       public void actionPerformed(ActionEvent e)\r
1090       {\r
1091         hiddenMarkers_actionPerformed(e);\r
1092       }\r
1093     });\r
1094     invertColSel.setText("Invert Column Selection");\r
1095     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1096         event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false));\r
1097     invertColSel.addActionListener(new ActionListener()\r
1098     {\r
1099       public void actionPerformed(ActionEvent e)\r
1100       {\r
1101         invertColSel_actionPerformed(e);\r
1102       }\r
1103     });\r
1104     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1105     {\r
1106         public void stateChanged(ChangeEvent evt)\r
1107         {\r
1108             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1109             int sel = pane.getSelectedIndex();\r
1110             tabSelectionChanged(sel);\r
1111         }\r
1112     });\r
1113     tabbedPane.addMouseListener(new MouseAdapter()\r
1114     {\r
1115       public void mousePressed(MouseEvent e)\r
1116       {\r
1117         tabbedPane_mousePressed(e);\r
1118       }\r
1119     });\r
1120     tabbedPane.addFocusListener(new FocusAdapter()\r
1121     {\r
1122       public void focusGained(FocusEvent e)\r
1123       {\r
1124         tabbedPane_focusGained(e);\r
1125       }\r
1126     });\r
1127     save.setText("Save");\r
1128     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1129         KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
1130     save.addActionListener(new ActionListener()\r
1131     {\r
1132       public void actionPerformed(ActionEvent e)\r
1133       {\r
1134         save_actionPerformed(e);\r
1135       }\r
1136     });\r
1137 \r
1138     alignFrameMenuBar.add(fileMenu);\r
1139     alignFrameMenuBar.add(editMenu);\r
1140     alignFrameMenuBar.add(searchMenu);\r
1141     alignFrameMenuBar.add(viewMenu);\r
1142     alignFrameMenuBar.add(colourMenu);\r
1143     alignFrameMenuBar.add(calculateMenu);\r
1144     alignFrameMenuBar.add(webService);\r
1145     fileMenu.add(addSequenceMenu);\r
1146     fileMenu.add(fetchSequence);\r
1147     fileMenu.addSeparator();\r
1148     fileMenu.add(vamsasStore);\r
1149     fileMenu.add(save);\r
1150     fileMenu.add(saveAs);\r
1151     fileMenu.add(outputTextboxMenu);\r
1152     fileMenu.add(printMenuItem);\r
1153     fileMenu.addSeparator();\r
1154     fileMenu.add(jMenu2);\r
1155     fileMenu.add(exportFeatures);\r
1156     fileMenu.add(exportAnnotations);\r
1157     fileMenu.add(LoadtreeMenuItem);\r
1158     fileMenu.add(associatedData);\r
1159     fileMenu.addSeparator();\r
1160     fileMenu.add(closeMenuItem);\r
1161     editMenu.add(undoMenuItem);\r
1162     editMenu.add(redoMenuItem);\r
1163     editMenu.add(cut);\r
1164     editMenu.add(copy);\r
1165     editMenu.add(jMenu1);\r
1166     editMenu.add(delete);\r
1167     editMenu.addSeparator();\r
1168     editMenu.add(selectAllSequenceMenuItem);\r
1169     editMenu.add(deselectAllSequenceMenuItem);\r
1170     editMenu.add(invertSequenceMenuItem);\r
1171     editMenu.add(invertColSel);\r
1172     editMenu.add(deleteGroups);\r
1173     editMenu.addSeparator();\r
1174     editMenu.add(remove2LeftMenuItem);\r
1175     editMenu.add(remove2RightMenuItem);\r
1176     editMenu.add(removeGappedColumnMenuItem);\r
1177     editMenu.add(removeAllGapsMenuItem);\r
1178     editMenu.add(removeRedundancyMenuItem);\r
1179     editMenu.addSeparator();\r
1180     editMenu.add(padGapsMenuitem);\r
1181     searchMenu.add(findMenuItem);\r
1182     viewMenu.add(font);\r
1183     viewMenu.add(smoothFont);\r
1184     viewMenu.addSeparator();\r
1185     viewMenu.add(jMenu3);\r
1186     viewMenu.add(hideMenu);\r
1187     viewMenu.add(hiddenMarkers);\r
1188     viewMenu.addSeparator();\r
1189     viewMenu.add(wrapMenuItem);\r
1190     viewMenu.add(seqLimits);\r
1191     viewMenu.add(scaleAbove);\r
1192     viewMenu.add(scaleLeft);\r
1193     viewMenu.add(scaleRight);\r
1194     viewMenu.add(viewBoxesMenuItem);\r
1195     viewMenu.add(viewTextMenuItem);\r
1196     viewMenu.add(colourTextMenuItem);\r
1197     viewMenu.add(renderGapsMenuItem);\r
1198     viewMenu.add(annotationPanelMenuItem);\r
1199     viewMenu.addSeparator();\r
1200     viewMenu.add(showSeqFeatures);\r
1201     viewMenu.add(featureSettings);\r
1202     viewMenu.addSeparator();\r
1203     viewMenu.add(overviewMenuItem);\r
1204     colourMenu.add(applyToAllGroups);\r
1205     colourMenu.addSeparator();\r
1206     colourMenu.add(noColourmenuItem);\r
1207     colourMenu.add(clustalColour);\r
1208     colourMenu.add(BLOSUM62Colour);\r
1209     colourMenu.add(PIDColour);\r
1210     colourMenu.add(zappoColour);\r
1211     colourMenu.add(taylorColour);\r
1212     colourMenu.add(hydrophobicityColour);\r
1213     colourMenu.add(helixColour);\r
1214     colourMenu.add(strandColour);\r
1215     colourMenu.add(turnColour);\r
1216     colourMenu.add(buriedColour);\r
1217     colourMenu.add(nucleotideColour);\r
1218     colourMenu.add(userDefinedColour);\r
1219     colourMenu.addSeparator();\r
1220     colourMenu.add(conservationMenuItem);\r
1221     colourMenu.add(modifyConservation);\r
1222     colourMenu.add(abovePIDThreshold);\r
1223     colourMenu.add(modifyPID);\r
1224     colourMenu.add(annotationColour);\r
1225     calculateMenu.add(sort);\r
1226     calculateMenu.add(calculate);\r
1227     calculateMenu.addSeparator();\r
1228     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1229     calculateMenu.add(PCAMenuItem);\r
1230     calculateMenu.addSeparator();\r
1231     calculateMenu.add(showTranslation);\r
1232     calculateMenu.add(autoCalculate);\r
1233     webServiceNoServices=new JMenuItem("<No Services>");\r
1234     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1235     jMenu1.add(pasteThis);\r
1236     sort.add(sortIDMenuItem);\r
1237     sort.add(sortGroupMenuItem);\r
1238     sort.add(sortPairwiseMenuItem);\r
1239     calculate.add(averageDistanceTreeMenuItem);\r
1240     calculate.add(neighbourTreeMenuItem);\r
1241     calculate.add(avDistanceTreeBlosumMenuItem);\r
1242     calculate.add(njTreeBlosumMenuItem);\r
1243     jMenu2.add(htmlMenuItem);\r
1244     jMenu2.add(epsFile);\r
1245     jMenu2.add(createPNG);\r
1246     addSequenceMenu.add(addFromFile);\r
1247     addSequenceMenu.add(addFromText);\r
1248     addSequenceMenu.add(addFromURL);\r
1249     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1250     statusPanel.add(statusBar, null);\r
1251     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1252     jMenu3.add(showAllColumns);\r
1253     jMenu3.add(showAllSeqs);\r
1254     hideMenu.add(hideSelColumns);\r
1255     hideMenu.add(hideSelSequences);\r
1256   }\r
1257 \r
1258   protected void outputText_actionPerformed(ActionEvent e)\r
1259   {\r
1260   }\r
1261 \r
1262   public void addFromFile_actionPerformed(ActionEvent e)\r
1263   {\r
1264 \r
1265   }\r
1266 \r
1267   public void addFromText_actionPerformed(ActionEvent e)\r
1268   {\r
1269 \r
1270   }\r
1271 \r
1272   public void addFromURL_actionPerformed(ActionEvent e)\r
1273   {\r
1274 \r
1275   }\r
1276 \r
1277   public void exportFeatures_actionPerformed(ActionEvent e)\r
1278   {\r
1279 \r
1280   }\r
1281 \r
1282   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1283   {\r
1284 \r
1285   }\r
1286 \r
1287   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1288   {\r
1289   }\r
1290 \r
1291   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1292   {\r
1293   }\r
1294 \r
1295   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1296   {\r
1297   }\r
1298 \r
1299   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1300   {\r
1301   }\r
1302 \r
1303   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1304   {\r
1305   }\r
1306 \r
1307   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1308   {\r
1309   }\r
1310 \r
1311   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1312   {\r
1313   }\r
1314 \r
1315   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1316   {\r
1317   }\r
1318 \r
1319   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1320   {\r
1321   }\r
1322 \r
1323   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1324   {\r
1325   }\r
1326 \r
1327   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1328   {\r
1329   }\r
1330 \r
1331   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1332   {\r
1333   }\r
1334 \r
1335   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1336   {\r
1337   }\r
1338 \r
1339   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1340   {\r
1341   }\r
1342 \r
1343   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1344   {\r
1345   }\r
1346 \r
1347   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1348   {\r
1349   }\r
1350 \r
1351   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1352   {\r
1353   }\r
1354 \r
1355   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1356   {\r
1357   }\r
1358 \r
1359   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1360   {\r
1361   }\r
1362 \r
1363   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1364   {\r
1365   }\r
1366 \r
1367   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1368   {\r
1369   }\r
1370 \r
1371   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1372   {\r
1373   }\r
1374 \r
1375   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1376   {\r
1377   }\r
1378 \r
1379   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1380   {\r
1381   }\r
1382 \r
1383   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1384   {\r
1385   }\r
1386 \r
1387   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1388   {\r
1389   }\r
1390 \r
1391   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1392   {\r
1393   }\r
1394 \r
1395   protected void clustalColour_actionPerformed(ActionEvent e)\r
1396   {\r
1397   }\r
1398 \r
1399   protected void zappoColour_actionPerformed(ActionEvent e)\r
1400   {\r
1401   }\r
1402 \r
1403   protected void taylorColour_actionPerformed(ActionEvent e)\r
1404   {\r
1405   }\r
1406 \r
1407   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1408   {\r
1409   }\r
1410 \r
1411   protected void helixColour_actionPerformed(ActionEvent e)\r
1412   {\r
1413   }\r
1414 \r
1415   protected void strandColour_actionPerformed(ActionEvent e)\r
1416   {\r
1417   }\r
1418 \r
1419   protected void turnColour_actionPerformed(ActionEvent e)\r
1420   {\r
1421   }\r
1422 \r
1423   protected void buriedColour_actionPerformed(ActionEvent e)\r
1424   {\r
1425   }\r
1426 \r
1427   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1428   {\r
1429   }\r
1430 \r
1431   protected void PIDColour_actionPerformed(ActionEvent e)\r
1432   {\r
1433   }\r
1434 \r
1435   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1436   {\r
1437   }\r
1438 \r
1439   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1440   {\r
1441   }\r
1442 \r
1443   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1444   {\r
1445   }\r
1446 \r
1447   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1448   {\r
1449   }\r
1450 \r
1451   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1452   {\r
1453   }\r
1454 \r
1455   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1456   {\r
1457   }\r
1458 \r
1459   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1460   {\r
1461   }\r
1462 \r
1463   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1464   {\r
1465   }\r
1466 \r
1467   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void copy_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   protected void cut_actionPerformed(ActionEvent e)\r
1480   {\r
1481   }\r
1482 \r
1483   protected void delete_actionPerformed(ActionEvent e)\r
1484   {\r
1485   }\r
1486 \r
1487   protected void pasteNew_actionPerformed(ActionEvent e)\r
1488   {\r
1489   }\r
1490 \r
1491   protected void pasteThis_actionPerformed(ActionEvent e)\r
1492   {\r
1493   }\r
1494 \r
1495   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1496   {\r
1497   }\r
1498 \r
1499   public void createPNG(java.io.File f)\r
1500   {\r
1501   }\r
1502 \r
1503   protected void font_actionPerformed(ActionEvent e)\r
1504   {\r
1505   }\r
1506 \r
1507   protected void seqLimit_actionPerformed(ActionEvent e)\r
1508   {\r
1509   }\r
1510 \r
1511   public void seqDBRef_actionPerformed(ActionEvent e)\r
1512   {\r
1513 \r
1514   }\r
1515 \r
1516 \r
1517   public void createEPS(java.io.File f)\r
1518   {\r
1519   }\r
1520 \r
1521   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1522   {\r
1523   }\r
1524 \r
1525   protected void jpred_actionPerformed(ActionEvent e)\r
1526   {\r
1527   }\r
1528 \r
1529   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1530   {\r
1531   }\r
1532 \r
1533   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1534   {\r
1535   }\r
1536 \r
1537   protected void scaleRight_actionPerformed(ActionEvent e)\r
1538   {\r
1539   }\r
1540 \r
1541   protected void modifyPID_actionPerformed(ActionEvent e)\r
1542   {\r
1543   }\r
1544 \r
1545   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1546   {\r
1547   }\r
1548 \r
1549 \r
1550 \r
1551   protected void saveAs_actionPerformed(ActionEvent e)\r
1552   {\r
1553   }\r
1554 \r
1555   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1556   {\r
1557   }\r
1558 \r
1559 \r
1560   public void vamsasStore_actionPerformed(ActionEvent e)\r
1561   {\r
1562 \r
1563   }\r
1564 \r
1565   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1566   {\r
1567 \r
1568   }\r
1569 \r
1570   public void showTranslation_actionPerformed(ActionEvent e)\r
1571   {\r
1572 \r
1573   }\r
1574 \r
1575   public void featureSettings_actionPerformed(ActionEvent e)\r
1576   {\r
1577 \r
1578   }\r
1579 \r
1580   public void fetchSequence_actionPerformed(ActionEvent e)\r
1581   {\r
1582 \r
1583   }\r
1584 \r
1585   public void smoothFont_actionPerformed(ActionEvent e)\r
1586   {\r
1587 \r
1588   }\r
1589 \r
1590   public void annotationColour_actionPerformed(ActionEvent e)\r
1591   {\r
1592 \r
1593   }\r
1594 \r
1595 \r
1596   public void associatedData_actionPerformed(ActionEvent e)\r
1597   {\r
1598 \r
1599   }\r
1600 \r
1601   public void autoCalculate_actionPerformed(ActionEvent e)\r
1602   {\r
1603 \r
1604   }\r
1605 \r
1606   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1607   {\r
1608 \r
1609   }\r
1610 \r
1611   public void showAllColumns_actionPerformed(ActionEvent e)\r
1612   {\r
1613 \r
1614   }\r
1615 \r
1616   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1617   {\r
1618 \r
1619   }\r
1620 \r
1621   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1622   {\r
1623 \r
1624   }\r
1625 \r
1626   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1627   {\r
1628 \r
1629   }\r
1630 \r
1631   public void findPdbId_actionPerformed(ActionEvent e)\r
1632   {\r
1633 \r
1634   }\r
1635 \r
1636   public void enterPdbId_actionPerformed(ActionEvent e)\r
1637   {\r
1638 \r
1639   }\r
1640 \r
1641   public void pdbFile_actionPerformed(ActionEvent e)\r
1642   {\r
1643 \r
1644   }\r
1645 \r
1646   public void invertColSel_actionPerformed(ActionEvent e)\r
1647   {\r
1648 \r
1649   }\r
1650 \r
1651   public void tabSelectionChanged(int sel)\r
1652   {\r
1653 \r
1654   }\r
1655 \r
1656   public void tabbedPane_mousePressed(MouseEvent e)\r
1657   {\r
1658 \r
1659   }\r
1660 \r
1661   public void tabbedPane_focusGained(FocusEvent e)\r
1662   {\r
1663     requestFocus();\r
1664   }\r
1665 \r
1666   public void save_actionPerformed(ActionEvent e)\r
1667   {\r
1668 \r
1669   }\r
1670 }\r