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JAL-3210 Barebones gradle/buildship/eclipse. See README
[jalview.git]
/
src
/
jalview
/
jbgui
/
GAlignFrame.java
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
9de31ab
..
6685c67
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-25,7
+25,6
@@
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;
@@
-36,7
+35,6
@@
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;
@@
-222,7
+220,7
@@
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.getAppID("alignment"));
+ setName("jalview-alignment");
jbInit();
setJMenuBar(alignFrameMenuBar);
jbInit();
setJMenuBar(alignFrameMenuBar);
@@
-278,14
+276,14
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-308,7
+306,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-335,7
+333,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-371,7
+369,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-385,7
+383,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-399,7
+397,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-413,8
+411,8
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-521,7
+519,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-545,11
+543,7
@@
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); 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.setBackground(Color.white);
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"));
@@
-560,7
+554,7
@@
public class GAlignFrame extends JInternalFrame
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem
- .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
+ .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
@@
-700,7
+694,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-714,7
+708,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-738,7
+732,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-764,7
+758,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), 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()
@@
-925,7
+919,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-950,7
+944,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-964,8
+958,8
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-979,7
+973,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
al = new ActionListener()
{
@@
-993,7
+987,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1019,8
+1013,8
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-1035,7
+1029,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1069,7
+1063,7
@@
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(Preferences.SHOW_JVSUFFIX, true));
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
@Override
seqLimits.addActionListener(new ActionListener()
{
@Override
@@
-1220,7
+1214,7
@@
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(Preferences.PAD_GAPS, false));
+ .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
@@
-1247,7
+1241,8
@@
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.getCodeTables())
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
{
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
showTranslation.add(item);
{
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
showTranslation.add(item);
@@
-1363,7
+1358,7
@@
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(Preferences.AUTO_CALC_CONSENSUS, true));
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
autoCalculate.addActionListener(new ActionListener()
{
@Override
@@
-1377,8
+1372,7
@@
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(Preferences.SORT_BY_TREE,
- false));
+ .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
sortByTree.addActionListener(new ActionListener()
{
@Override
@@
-1552,8
+1546,8
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
false);
al = new ActionListener()
{
false);
al = new ActionListener()
{
@@
-1616,7
+1610,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override
@@
-1641,7
+1635,7
@@
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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
al = new ActionListener()
{
@Override