X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=9de31aba717f37f2085d8b09f9af6dc25339cf3f;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=6685c67c589abf56cf914af2d41a4089f1a0f1c9;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6685c67..9de31ab 100755 --- 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.bin.Jalview; 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.Toolkit; 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 - setName("jalview-alignment"); + setName(Jalview.getAppID("alignment")); 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, - 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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)); - 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")); @@ -554,7 +560,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -694,7 +700,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -708,7 +714,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -732,7 +738,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -758,7 +764,7 @@ public class GAlignFrame extends JInternalFrame 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() @@ -919,7 +925,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -944,7 +950,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -958,8 +964,8 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -973,7 +979,7 @@ public class GAlignFrame extends JInternalFrame copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @@ -987,7 +993,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override @@ -1063,7 +1069,7 @@ public class GAlignFrame extends JInternalFrame }); 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 @@ -1214,7 +1220,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -1241,8 +1247,7 @@ public class GAlignFrame extends JInternalFrame 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); @@ -1358,7 +1363,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -1372,7 +1377,8 @@ public class GAlignFrame extends JInternalFrame sortByTree.setToolTipText("" + 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 @@ -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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.ALT_MASK, 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override