Class MenuCreator
- java.lang.Object
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- org.biojava.nbio.structure.align.gui.MenuCreator
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public class MenuCreator extends java.lang.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 java.lang.String
ALIGNMENT_PANEL
static java.lang.String
DIST_MATRICES
static java.lang.String
DOT_PLOT
static java.lang.String
EQR_COLOR
static java.lang.String
FASTA_FORMAT
static java.lang.String
FATCAT_BLOCK
static java.lang.String
FATCAT_TEXT
protected static int
keyMask
static java.lang.String
LOAD_ALIGNMENT_XML
static java.lang.String
LOAD_DB_RESULTS
static java.lang.String
MULTIPLE_ALIGN
static java.lang.String
PAIRS_ONLY
static java.lang.String
PAIRWISE_ALIGN
static java.lang.String
PHYLOGENETIC_TREE
static java.lang.String
PRINT
static java.lang.String
SAVE_ALIGNMENT_XML
static java.lang.String
SELECT_EQR
static java.lang.String
SIMILARITY_COLOR
static java.lang.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 javax.swing.ImageIcon
createImageIcon(java.lang.String path)
Returns an ImageIcon, or null if the path was invalid.static javax.swing.JMenuItem
getAboutMenuItem()
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.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.static javax.swing.JMenuItem
getCloseMenuItem(javax.swing.JFrame frame)
static javax.swing.JMenuItem
getDBResultMenuItem()
static javax.swing.JMenuItem
getExitMenuItem()
static javax.swing.JMenuItem
getExportPDBMenuItem(AbstractAlignmentJmol parent)
static javax.swing.JMenuItem
getHelpMenuItem()
protected static javax.swing.JMenuItem
getIcon(java.awt.event.ActionListener actionListener, java.lang.String text)
static javax.swing.JMenuItem
getLoadMenuItem()
protected static javax.swing.JMenuItem
getMultipleAlignmentMenuItem()
static javax.swing.JMenuItem
getOpenPDBMenuItem()
protected static javax.swing.JMenuItem
getPairwiseAlignmentMenuItem()
static javax.swing.JMenuItem
getPrintMenuItem()
static javax.swing.JMenuItem
getSaveAlignmentMenuItem(AFPChain afpChain, MultipleAlignment msa)
static javax.swing.JMenuItem
getShowPDBMenuItem()
static javax.swing.JMenuBar
initAlignmentGUIMenu(javax.swing.JFrame frame)
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.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 java.lang.String PRINT
- See Also:
- Constant Field Values
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ALIGNMENT_PANEL
public static final java.lang.String ALIGNMENT_PANEL
- See Also:
- Constant Field Values
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TEXT_ONLY
public static final java.lang.String TEXT_ONLY
- See Also:
- Constant Field Values
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PAIRS_ONLY
public static final java.lang.String PAIRS_ONLY
- See Also:
- Constant Field Values
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SELECT_EQR
public static final java.lang.String SELECT_EQR
- See Also:
- Constant Field Values
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SIMILARITY_COLOR
public static final java.lang.String SIMILARITY_COLOR
- See Also:
- Constant Field Values
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EQR_COLOR
public static final java.lang.String EQR_COLOR
- See Also:
- Constant Field Values
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FATCAT_BLOCK
public static final java.lang.String FATCAT_BLOCK
- See Also:
- Constant Field Values
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LOAD_DB_RESULTS
public static final java.lang.String LOAD_DB_RESULTS
- See Also:
- Constant Field Values
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SAVE_ALIGNMENT_XML
public static final java.lang.String SAVE_ALIGNMENT_XML
- See Also:
- Constant Field Values
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LOAD_ALIGNMENT_XML
public static final java.lang.String LOAD_ALIGNMENT_XML
- See Also:
- Constant Field Values
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FATCAT_TEXT
public static final java.lang.String FATCAT_TEXT
- See Also:
- Constant Field Values
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FASTA_FORMAT
public static final java.lang.String FASTA_FORMAT
- See Also:
- Constant Field Values
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DIST_MATRICES
public static final java.lang.String DIST_MATRICES
- See Also:
- Constant Field Values
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DOT_PLOT
public static final java.lang.String DOT_PLOT
- See Also:
- Constant Field Values
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PAIRWISE_ALIGN
public static final java.lang.String PAIRWISE_ALIGN
- See Also:
- Constant Field Values
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MULTIPLE_ALIGN
public static final java.lang.String MULTIPLE_ALIGN
- See Also:
- Constant Field Values
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PHYLOGENETIC_TREE
public static final java.lang.String PHYLOGENETIC_TREE
- See Also:
- Constant Field Values
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keyMask
protected static final int keyMask
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Method Detail
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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
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getDBResultMenuItem
public static javax.swing.JMenuItem getDBResultMenuItem()
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getShowPDBMenuItem
public static javax.swing.JMenuItem getShowPDBMenuItem()
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getOpenPDBMenuItem
public static javax.swing.JMenuItem getOpenPDBMenuItem()
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getLoadMenuItem
public static javax.swing.JMenuItem getLoadMenuItem()
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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
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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
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getIcon
protected static javax.swing.JMenuItem getIcon(java.awt.event.ActionListener actionListener, java.lang.String text)
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getPrintMenuItem
public static javax.swing.JMenuItem getPrintMenuItem()
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getExportPDBMenuItem
public static javax.swing.JMenuItem getExportPDBMenuItem(AbstractAlignmentJmol parent)
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getSaveAlignmentMenuItem
public static javax.swing.JMenuItem getSaveAlignmentMenuItem(AFPChain afpChain, MultipleAlignment msa)
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getAboutMenuItem
public static javax.swing.JMenuItem getAboutMenuItem()
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getExitMenuItem
public static javax.swing.JMenuItem getExitMenuItem()
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getHelpMenuItem
public static javax.swing.JMenuItem getHelpMenuItem()
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getCloseMenuItem
public static javax.swing.JMenuItem getCloseMenuItem(javax.swing.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 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
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getPairwiseAlignmentMenuItem
protected static javax.swing.JMenuItem getPairwiseAlignmentMenuItem()
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getMultipleAlignmentMenuItem
protected static javax.swing.JMenuItem getMultipleAlignmentMenuItem()
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initAlignmentGUIMenu
public static javax.swing.JMenuBar initAlignmentGUIMenu(javax.swing.JFrame frame)
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showMemoryMonitor
protected static void showMemoryMonitor()
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