Field Detail

• PRINT

  public static final java.lang.String PRINT

  See Also:

  Constant Field Values

• ALIGNMENT_PANEL

  public static final java.lang.String ALIGNMENT_PANEL

  See Also:

  Constant Field Values

• TEXT_ONLY

  public static final java.lang.String TEXT_ONLY

  See Also:

  Constant Field Values

• PAIRS_ONLY

  public static final java.lang.String PAIRS_ONLY

  See Also:

  Constant Field Values

• SELECT_EQR

  public static final java.lang.String SELECT_EQR

  See Also:

  Constant Field Values

• SIMILARITY_COLOR

  public static final java.lang.String SIMILARITY_COLOR

  See Also:

  Constant Field Values

• EQR_COLOR

  public static final java.lang.String EQR_COLOR

  See Also:

  Constant Field Values

• FATCAT_BLOCK

  public static final java.lang.String FATCAT_BLOCK

  See Also:

  Constant Field Values

• LOAD_DB_RESULTS

  public static final java.lang.String LOAD_DB_RESULTS

  See Also:

  Constant Field Values

• SAVE_ALIGNMENT_XML

  public static final java.lang.String SAVE_ALIGNMENT_XML

  See Also:

  Constant Field Values

• LOAD_ALIGNMENT_XML

  public static final java.lang.String LOAD_ALIGNMENT_XML

  See Also:

  Constant Field Values

• FATCAT_TEXT

  public static final java.lang.String FATCAT_TEXT

  See Also:

  Constant Field Values

• FASTA_FORMAT

  public static final java.lang.String FASTA_FORMAT

  See Also:

  Constant Field Values

• DIST_MATRICES

  public static final java.lang.String DIST_MATRICES

  See Also:

  Constant Field Values

• DOT_PLOT

  public static final java.lang.String DOT_PLOT

  See Also:

  Constant Field Values

• PAIRWISE_ALIGN

  public static final java.lang.String PAIRWISE_ALIGN

  See Also:

  Constant Field Values

• MULTIPLE_ALIGN

  public static final java.lang.String MULTIPLE_ALIGN

  See Also:

  Constant Field Values

• PHYLOGENETIC_TREE

  public static final java.lang.String PHYLOGENETIC_TREE

  See Also:

  Constant Field Values

• keyMask

  protected static final int keyMask

Constructor Detail

• MenuCreator

  public MenuCreator()

Method Detail

• initJmolMenu

  public static javax.swing.JMenuBar initJmolMenu​(javax.swing.JFrame frame,
                                                  AbstractAlignmentJmol parent,
                                                  AFPChain afpChain,
                                                  MultipleAlignment msa)

  Provide a JMenuBar that can be added to a JFrame containing a JmolPanel. The alignment has to be either an AFPChain or a MultipleAlignment: set the other parameter to null.

  Menus included:

  • File: open, save, export, import, exit.
  • Align: new pairwise alignment, new multiple alignment.
  • View: aligment panel, aligned pairs, text format, FatCat format, distance matrices, dot plot.
  • Help

  Returns:

  a JMenuBar

• getDBResultMenuItem

  public static javax.swing.JMenuItem getDBResultMenuItem()

• getShowPDBMenuItem

  public static javax.swing.JMenuItem getShowPDBMenuItem()

• getOpenPDBMenuItem

  public static javax.swing.JMenuItem getOpenPDBMenuItem()

• getLoadMenuItem

  public static javax.swing.JMenuItem getLoadMenuItem()

• getAlignmentPanelMenu

  public static javax.swing.JMenuBar getAlignmentPanelMenu​(javax.swing.JFrame frame,
                                                           java.awt.event.ActionListener actionListener,
                                                           AFPChain afpChain,
                                                           MultipleAlignment msa)

  Create the menu for the Alignment Panel representation of Structural Alignments. The alignment can be in AFPChain format or in the MultipleAlignment format.

  Parameters:

  frame -

  actionListener -

  afpChain -

  MultipleAlignment -

  Returns:

  a JMenuBar

• getAlignmentTextMenu

  public static javax.swing.JMenuBar getAlignmentTextMenu​(javax.swing.JFrame frame,
                                                          java.awt.event.ActionListener actionListener,
                                                          AFPChain afpChain,
                                                          MultipleAlignment msa)

  Create the menu for the Text representations of Structural Alignments.

  Parameters:

  frame -

  actionListener -

  afpChain -

  msa -

  Returns:

  a JMenuBar

• getIcon

  protected static javax.swing.JMenuItem getIcon​(java.awt.event.ActionListener actionListener,
                                                 java.lang.String text)

• getPrintMenuItem

  public static javax.swing.JMenuItem getPrintMenuItem()

• getExportPDBMenuItem

  public static javax.swing.JMenuItem getExportPDBMenuItem​(AbstractAlignmentJmol parent)

• getSaveAlignmentMenuItem

  public static javax.swing.JMenuItem getSaveAlignmentMenuItem​(AFPChain afpChain,
                                                               MultipleAlignment msa)

• getAboutMenuItem

  public static javax.swing.JMenuItem getAboutMenuItem()

• getExitMenuItem

  public static javax.swing.JMenuItem getExitMenuItem()

• getHelpMenuItem

  public static javax.swing.JMenuItem getHelpMenuItem()

• getCloseMenuItem

  public static javax.swing.JMenuItem getCloseMenuItem​(javax.swing.JFrame frame)

• showAboutDialog

  public static void showAboutDialog()

  Show some info about this GUI

• showSystemInfo

  public static void showSystemInfo()

• createImageIcon

  public static javax.swing.ImageIcon createImageIcon​(java.lang.String path)

  Returns an ImageIcon, or null if the path was invalid.

  Parameters:

  path - the path to the icon

  Returns:

  ImageIcon object

• getPairwiseAlignmentMenuItem

  protected static javax.swing.JMenuItem getPairwiseAlignmentMenuItem()

• getMultipleAlignmentMenuItem

  protected static javax.swing.JMenuItem getMultipleAlignmentMenuItem()

• initAlignmentGUIMenu

  public static javax.swing.JMenuBar initAlignmentGUIMenu​(javax.swing.JFrame frame)

• showMemoryMonitor

  protected static void showMemoryMonitor()