Class MenuCreator
- java.lang.Object
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- org.biojava.nbio.structure.align.gui.MenuCreator
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public class MenuCreator extends Object
Create the menus for structure alignment GUI windows (JFrames).Examples: Text Frames, Alignment Panels, Jmol Panels.
- Since:
- 1.7
- Author:
- Andreas Prlic, Aleix Lafita, Spencer Bliven
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MenuCreator.DotPlotListener
Creates a frame to display a DotPlotPanel.
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Field Summary
Fields Modifier and Type Field Description static String
ALIGNMENT_PANEL
static String
DIST_MATRICES
static String
DOT_PLOT
static String
EQR_COLOR
static String
FASTA_FORMAT
static String
FATCAT_BLOCK
static String
FATCAT_TEXT
protected static int
keyMask
static String
LOAD_ALIGNMENT_XML
static String
LOAD_DB_RESULTS
static String
MULTIPLE_ALIGN
static String
PAIRS_ONLY
static String
PAIRWISE_ALIGN
static String
PHYLOGENETIC_TREE
static String
PRINT
static String
SAVE_ALIGNMENT_XML
static String
SELECT_EQR
static String
SIMILARITY_COLOR
static String
TEXT_ONLY
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Constructor Summary
Constructors Constructor Description MenuCreator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static ImageIcon
createImageIcon(String path)
Returns an ImageIcon, or null if the path was invalid.static JMenuItem
getAboutMenuItem()
static JMenuBar
getAlignmentPanelMenu(JFrame frame, ActionListener actionListener, AFPChain afpChain, MultipleAlignment msa)
Create the menu for the Alignment Panel representation of Structural Alignments.static JMenuBar
getAlignmentTextMenu(JFrame frame, ActionListener actionListener, AFPChain afpChain, MultipleAlignment msa)
Create the menu for the Text representations of Structural Alignments.static JMenuItem
getCloseMenuItem(JFrame frame)
static JMenuItem
getDBResultMenuItem()
static JMenuItem
getExitMenuItem()
static JMenuItem
getExportPDBMenuItem(AbstractAlignmentJmol parent)
static JMenuItem
getHelpMenuItem()
protected static JMenuItem
getIcon(ActionListener actionListener, String text)
static JMenuItem
getLoadMenuItem()
protected static JMenuItem
getMultipleAlignmentMenuItem()
static JMenuItem
getOpenPDBMenuItem()
protected static JMenuItem
getPairwiseAlignmentMenuItem()
static JMenuItem
getPrintMenuItem()
static JMenuItem
getSaveAlignmentMenuItem(AFPChain afpChain, MultipleAlignment msa)
static JMenuItem
getShowPDBMenuItem()
static JMenuBar
initAlignmentGUIMenu(JFrame frame)
static JMenuBar
initJmolMenu(JFrame frame, AbstractAlignmentJmol parent, AFPChain afpChain, MultipleAlignment msa)
Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.static void
showAboutDialog()
Show some info about this GUIprotected static void
showMemoryMonitor()
static void
showSystemInfo()
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Field Detail
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PRINT
public static final String PRINT
- See Also:
- Constant Field Values
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ALIGNMENT_PANEL
public static final String ALIGNMENT_PANEL
- See Also:
- Constant Field Values
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TEXT_ONLY
public static final String TEXT_ONLY
- See Also:
- Constant Field Values
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PAIRS_ONLY
public static final String PAIRS_ONLY
- See Also:
- Constant Field Values
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SELECT_EQR
public static final String SELECT_EQR
- See Also:
- Constant Field Values
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SIMILARITY_COLOR
public static final String SIMILARITY_COLOR
- See Also:
- Constant Field Values
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EQR_COLOR
public static final String EQR_COLOR
- See Also:
- Constant Field Values
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FATCAT_BLOCK
public static final String FATCAT_BLOCK
- See Also:
- Constant Field Values
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LOAD_DB_RESULTS
public static final String LOAD_DB_RESULTS
- See Also:
- Constant Field Values
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SAVE_ALIGNMENT_XML
public static final String SAVE_ALIGNMENT_XML
- See Also:
- Constant Field Values
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LOAD_ALIGNMENT_XML
public static final String LOAD_ALIGNMENT_XML
- See Also:
- Constant Field Values
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FATCAT_TEXT
public static final String FATCAT_TEXT
- See Also:
- Constant Field Values
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FASTA_FORMAT
public static final String FASTA_FORMAT
- See Also:
- Constant Field Values
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DIST_MATRICES
public static final String DIST_MATRICES
- See Also:
- Constant Field Values
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DOT_PLOT
public static final String DOT_PLOT
- See Also:
- Constant Field Values
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PAIRWISE_ALIGN
public static final String PAIRWISE_ALIGN
- See Also:
- Constant Field Values
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MULTIPLE_ALIGN
public static final String MULTIPLE_ALIGN
- See Also:
- Constant Field Values
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PHYLOGENETIC_TREE
public static final String PHYLOGENETIC_TREE
- See Also:
- Constant Field Values
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keyMask
protected static final int keyMask
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Constructor Detail
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MenuCreator
public MenuCreator()
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Method Detail
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initJmolMenu
public static JMenuBar initJmolMenu(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
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getDBResultMenuItem
public static JMenuItem getDBResultMenuItem()
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getShowPDBMenuItem
public static JMenuItem getShowPDBMenuItem()
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getOpenPDBMenuItem
public static JMenuItem getOpenPDBMenuItem()
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getLoadMenuItem
public static JMenuItem getLoadMenuItem()
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getAlignmentPanelMenu
public static JMenuBar getAlignmentPanelMenu(JFrame frame, 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
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getAlignmentTextMenu
public static JMenuBar getAlignmentTextMenu(JFrame frame, ActionListener actionListener, AFPChain afpChain, MultipleAlignment msa)
Create the menu for the Text representations of Structural Alignments.- Parameters:
frame
-actionListener
-afpChain
-msa
-- Returns:
- a JMenuBar
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getIcon
protected static JMenuItem getIcon(ActionListener actionListener, String text)
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getPrintMenuItem
public static JMenuItem getPrintMenuItem()
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getExportPDBMenuItem
public static JMenuItem getExportPDBMenuItem(AbstractAlignmentJmol parent)
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getSaveAlignmentMenuItem
public static JMenuItem getSaveAlignmentMenuItem(AFPChain afpChain, MultipleAlignment msa)
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getAboutMenuItem
public static JMenuItem getAboutMenuItem()
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getExitMenuItem
public static JMenuItem getExitMenuItem()
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getHelpMenuItem
public static JMenuItem getHelpMenuItem()
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getCloseMenuItem
public static JMenuItem getCloseMenuItem(JFrame frame)
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showAboutDialog
public static void showAboutDialog()
Show some info about this GUI
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showSystemInfo
public static void showSystemInfo()
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createImageIcon
public static ImageIcon createImageIcon(String path)
Returns an ImageIcon, or null if the path was invalid.- Parameters:
path
- the path to the icon- Returns:
- ImageIcon object
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getPairwiseAlignmentMenuItem
protected static JMenuItem getPairwiseAlignmentMenuItem()
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getMultipleAlignmentMenuItem
protected static JMenuItem getMultipleAlignmentMenuItem()
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initAlignmentGUIMenu
public static JMenuBar initAlignmentGUIMenu(JFrame frame)
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showMemoryMonitor
protected static void showMemoryMonitor()
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