Package org.biojava.nbio.structure.align.gui

Class MenuCreator

java.lang.Object

org.biojava.nbio.structure.align.gui.MenuCreator

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MenuCreator.DotPlotListener	Creates a frame to display a DotPlotPanel.

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

Constructor Summary

Constructors

Constructor	Description
MenuCreator()

Method Summary

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, org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.align.multiple.MultipleAlignment msa)	Create the menu for the Alignment Panel representation of Structural Alignments.
static JMenuBar	getAlignmentTextMenu(JFrame frame, ActionListener actionListener, org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.align.multiple.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(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.align.multiple.MultipleAlignment msa)
static JMenuItem	getShowPDBMenuItem()
static JMenuBar	initAlignmentGUIMenu(JFrame frame)
static JMenuBar	initJmolMenu(JFrame frame, AbstractAlignmentJmol parent, org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.align.multiple.MultipleAlignment msa)	Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
static void	showAboutDialog()	Show some info about this GUI
protected static void	showMemoryMonitor()
static void	showSystemInfo()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PRINT

public static final String PRINT

See Also:

Constant Field Values

ALIGNMENT_PANEL

public static final String ALIGNMENT_PANEL

See Also:

Constant Field Values

TEXT_ONLY

public static final String TEXT_ONLY

See Also:

Constant Field Values

PAIRS_ONLY

public static final String PAIRS_ONLY

See Also:

Constant Field Values

SELECT_EQR

public static final String SELECT_EQR

See Also:

Constant Field Values

SIMILARITY_COLOR

public static final String SIMILARITY_COLOR

See Also:

Constant Field Values

EQR_COLOR

public static final String EQR_COLOR

See Also:

Constant Field Values

FATCAT_BLOCK

public static final String FATCAT_BLOCK

See Also:

Constant Field Values

LOAD_DB_RESULTS

public static final String LOAD_DB_RESULTS

See Also:

Constant Field Values

SAVE_ALIGNMENT_XML

public static final String SAVE_ALIGNMENT_XML

See Also:

Constant Field Values

LOAD_ALIGNMENT_XML

public static final String LOAD_ALIGNMENT_XML

See Also:

Constant Field Values

FATCAT_TEXT

public static final String FATCAT_TEXT

See Also:

Constant Field Values

FASTA_FORMAT

public static final String FASTA_FORMAT

See Also:

Constant Field Values

DIST_MATRICES

public static final String DIST_MATRICES

See Also:

Constant Field Values

DOT_PLOT

public static final String DOT_PLOT

See Also:

Constant Field Values

PAIRWISE_ALIGN

public static final String PAIRWISE_ALIGN

See Also:

Constant Field Values

MULTIPLE_ALIGN

public static final String MULTIPLE_ALIGN

See Also:

Constant Field Values

PHYLOGENETIC_TREE

public static final String PHYLOGENETIC_TREE

See Also:

Constant Field Values

keyMask

protected static final int keyMask

Constructor Detail

MenuCreator

public MenuCreator()

Method Detail

initJmolMenu

public static JMenuBar initJmolMenu(JFrame frame,
                                    AbstractAlignmentJmol parent,
                                    org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                    org.biojava.nbio.structure.align.multiple.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 JMenuItem getDBResultMenuItem()

getShowPDBMenuItem

public static JMenuItem getShowPDBMenuItem()

getOpenPDBMenuItem

public static JMenuItem getOpenPDBMenuItem()

getLoadMenuItem

public static JMenuItem getLoadMenuItem()

getAlignmentPanelMenu

public static JMenuBar getAlignmentPanelMenu(JFrame frame,
                                             ActionListener actionListener,
                                             org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                             org.biojava.nbio.structure.align.multiple.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 JMenuBar getAlignmentTextMenu(JFrame frame,
                                            ActionListener actionListener,
                                            org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                            org.biojava.nbio.structure.align.multiple.MultipleAlignment msa)

Create the menu for the Text representations of Structural Alignments.

Parameters:

frame -

actionListener -

afpChain -

msa -

Returns:

a JMenuBar

getIcon

protected static JMenuItem getIcon(ActionListener actionListener,
                                   String text)

getPrintMenuItem

public static JMenuItem getPrintMenuItem()

getExportPDBMenuItem

public static JMenuItem getExportPDBMenuItem(AbstractAlignmentJmol parent)

getSaveAlignmentMenuItem

public static JMenuItem getSaveAlignmentMenuItem(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                                 org.biojava.nbio.structure.align.multiple.MultipleAlignment msa)

getAboutMenuItem

public static JMenuItem getAboutMenuItem()

getExitMenuItem

public static JMenuItem getExitMenuItem()

getHelpMenuItem

public static JMenuItem getHelpMenuItem()

getCloseMenuItem

public static JMenuItem getCloseMenuItem(JFrame frame)

showAboutDialog

public static void showAboutDialog()

Show some info about this GUI

showSystemInfo

public static void showSystemInfo()

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

getPairwiseAlignmentMenuItem

protected static JMenuItem getPairwiseAlignmentMenuItem()

getMultipleAlignmentMenuItem

protected static JMenuItem getMultipleAlignmentMenuItem()

initAlignmentGUIMenu

public static JMenuBar initAlignmentGUIMenu(JFrame frame)

showMemoryMonitor

protected static void showMemoryMonitor()