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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git]
/
src
/
jalview
/
jbgui
/
GAlignFrame.java
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
6685c67
..
9de31ab
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-25,6
+25,7
@@
import jalview.analysis.GeneticCodeI;
import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
@@
-35,6
+36,7
@@
import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
+import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
@@
-220,7
+222,7
@@
public class GAlignFrame extends JInternalFrame
{
// for Web-page embedding using id=align-frame-div
{
// for Web-page embedding using id=align-frame-div
- setName("jalview-alignment");
+ setName(Jalview.getAppID("alignment"));
jbInit();
setJMenuBar(alignFrameMenuBar);
jbInit();
setJMenuBar(alignFrameMenuBar);
@@
-276,14
+278,14
@@
public class GAlignFrame extends JInternalFrame
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-306,7
+308,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-333,7
+335,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-369,7
+371,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-383,7
+385,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-397,7
+399,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-411,8
+413,8
@@
public class GAlignFrame extends JInternalFrame
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-519,7
+521,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-543,7
+545,11
@@
public class GAlignFrame extends JInternalFrame
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setBackground(Color.white);
+ // statusBar.setBackground(Color.white); BH 2019.08.01 -- this does nothing,
+ // as the label is not opaque
+ statusBar.setOpaque(true);// BH 2019.07.01 -- setting a label opaque avoids
+ // frame repaint in SwingJS and has no effect in
+ // Java
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
@@
-554,7
+560,7
@@
public class GAlignFrame extends JInternalFrame
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem
- .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
+ .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
@@
-694,7
+700,7
@@
public class GAlignFrame extends JInternalFrame
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-708,7
+714,7
@@
public class GAlignFrame extends JInternalFrame
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-732,7
+738,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-758,7
+764,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
@@
-919,7
+925,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-944,7
+950,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-958,8
+964,8
@@
public class GAlignFrame extends JInternalFrame
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-973,7
+979,7
@@
public class GAlignFrame extends JInternalFrame
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
al = new ActionListener()
{
@@
-987,7
+993,7
@@
public class GAlignFrame extends JInternalFrame
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1013,8
+1019,8
@@
public class GAlignFrame extends JInternalFrame
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-1029,7
+1035,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1063,7
+1069,7
@@
public class GAlignFrame extends JInternalFrame
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(jalview.bin.Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
seqLimits.addActionListener(new ActionListener()
{
@Override
seqLimits.addActionListener(new ActionListener()
{
@Override
@@
-1214,7
+1220,7
@@
public class GAlignFrame extends JInternalFrame
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ .setState(jalview.bin.Cache.getDefault(Preferences.PAD_GAPS, false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
@@
-1241,8
+1247,7
@@
public class GAlignFrame extends JInternalFrame
showTranslation
.setText(MessageManager.getString("label.translate_cDNA"));
boolean first = true;
showTranslation
.setText(MessageManager.getString("label.translate_cDNA"));
boolean first = true;
- for (final GeneticCodeI table : GeneticCodes.getInstance()
- .getCodeTables())
+ for (final GeneticCodeI table : GeneticCodes.getCodeTables())
{
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
showTranslation.add(item);
{
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
showTranslation.add(item);
@@
-1358,7
+1363,7
@@
public class GAlignFrame extends JInternalFrame
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ jalview.bin.Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
autoCalculate.addActionListener(new ActionListener()
{
@Override
@@
-1372,7
+1377,8
@@
public class GAlignFrame extends JInternalFrame
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ .setState(jalview.bin.Cache.getDefault(Preferences.SORT_BY_TREE,
+ false));
sortByTree.addActionListener(new ActionListener()
{
@Override
sortByTree.addActionListener(new ActionListener()
{
@Override
@@
-1546,8
+1552,8
@@
public class GAlignFrame extends JInternalFrame
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-1610,7
+1616,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1635,7
+1641,7
@@
public class GAlignFrame extends JInternalFrame
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override