X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6aaba84b7596d7424cf15feaec4c3b7326879715;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=69031d1612f302c25fa9bf03593d57b3631f96ea;hpb=5986040b8a7172172b8650e6a4c717af5bca277b;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 69031d1..6aaba84 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,19 +21,20 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +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; +import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; 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; @@ -60,15 +61,18 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +@SuppressWarnings("serial") public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenuItem closeMenuItem = new JMenuItem(); - protected JMenu webService = new JMenu(); + public JMenu webService = new JMenu();// BH 2019 was protected, but not + // sufficient for AlignFrame thread run - protected JMenuItem webServiceNoServices; + public JMenuItem webServiceNoServices;// BH 2019 was protected, but not + // sufficient for AlignFrame thread run protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); @@ -76,7 +80,9 @@ public class GAlignFrame extends JInternalFrame protected JMenu sortByAnnotScore = new JMenu(); - public JLabel statusBar = new JLabel(); + public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not + // sufficient for + // AlignFrame.printWriter protected JMenu outputTextboxMenu = new JMenu(); @@ -124,7 +130,7 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem modifyPID; - protected JMenuItem annotationColour; + protected JRadioButtonMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); @@ -138,7 +144,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); - protected JMenuItem showTranslation = new JMenuItem(); + protected JMenu showTranslation = new JMenu(); protected JMenuItem showReverse = new JMenuItem(); @@ -170,7 +176,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); - protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane(); + protected JTabbedPane tabbedPane = new JTabbedPane(); protected JMenuItem reload = new JMenuItem(); @@ -197,14 +203,14 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); - + protected JMenuItem openFeatureSettings; private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; - private Map accelerators = new HashMap(); + private Map accelerators = new HashMap<>(); private SplitContainerI splitFrame; @@ -212,6 +218,10 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName("jalview-alignment"); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -236,7 +246,7 @@ public class GAlignFrame extends JInternalFrame System.err.println(e.toString()); } - if (!Platform.isAMac()) + if (Platform.allowMnemonics()) // was "not mac and not JS" { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); @@ -266,14 +276,14 @@ public class GAlignFrame extends JInternalFrame // 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, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -296,7 +306,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -323,7 +333,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -359,7 +369,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -373,7 +383,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -387,7 +397,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -401,8 +411,8 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -509,7 +519,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -684,7 +694,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -698,7 +708,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -722,7 +732,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -748,7 +758,7 @@ public class GAlignFrame extends JInternalFrame 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() @@ -909,7 +919,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -934,7 +944,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -948,8 +958,8 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -963,27 +973,27 @@ public class GAlignFrame extends JInternalFrame copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); 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 public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -995,7 +1005,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1003,8 +1013,8 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -1019,7 +1029,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -1053,7 +1063,7 @@ public class GAlignFrame extends JInternalFrame }); seqLimits.setText( MessageManager.getString("label.show_sequence_limits")); - seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); + seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new ActionListener() { @Override @@ -1204,7 +1214,7 @@ public class GAlignFrame extends JInternalFrame padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); padGapsMenuitem - .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); + .setState(Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { @Override @@ -1224,16 +1234,33 @@ public class GAlignFrame extends JInternalFrame vamsasStore_actionPerformed(e); } }); + + /* + * Translate as cDNA with sub-menu of translation tables + */ showTranslation .setText(MessageManager.getString("label.translate_cDNA")); - showTranslation.addActionListener(new ActionListener() + boolean first = true; + for (final GeneticCodeI table : GeneticCodes.getInstance() + .getCodeTables()) { - @Override - public void actionPerformed(ActionEvent e) + JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); + showTranslation.add(item); + item.addActionListener(new ActionListener() { - showTranslation_actionPerformed(e); + @Override + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(table); + } + }); + if (first) + { + showTranslation.addSeparator(); } - }); + first = false; + } + showReverse.setText(MessageManager.getString("label.reverse")); showReverse.addActionListener(new ActionListener() { @@ -1284,7 +1311,6 @@ public class GAlignFrame extends JInternalFrame openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); - openFeatureSettings.setEnabled(false); openFeatureSettings.addActionListener(new ActionListener() { @Override @@ -1293,6 +1319,10 @@ public class GAlignFrame extends JInternalFrame featureSettings_actionPerformed(e); } }); + + /* + * add sub-menu of database we can fetch from + */ JMenuItem fetchSequence = new JMenuItem( MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() @@ -1300,7 +1330,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1314,7 +1344,8 @@ public class GAlignFrame extends JInternalFrame associatedData_actionPerformed(e); } }); - loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file")); + loadVcf = new JMenuItem( + MessageManager.getString("label.load_vcf_file")); loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); loadVcf.addActionListener(new ActionListener() { @@ -1327,7 +1358,7 @@ public class GAlignFrame extends JInternalFrame autoCalculate.setText( MessageManager.getString("label.autocalculate_consensus")); autoCalculate.setState( - jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + Cache.getDefault("AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { @Override @@ -1341,7 +1372,7 @@ 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(Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { @Override @@ -1515,8 +1546,8 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -1579,7 +1610,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -1604,7 +1635,7 @@ public class GAlignFrame extends JInternalFrame 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 @@ -1708,7 +1739,7 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - if (!Jalview.isJS()) + if (!Platform.isJS()) { alignFrameMenuBar.add(webService); } @@ -1729,7 +1760,7 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); - if (!Jalview.isJS()) + if (!Platform.isJS()) { fileMenu.add(loadVcf); } @@ -1766,11 +1797,8 @@ public class GAlignFrame extends JInternalFrame hideMenu.add(hideAllSelection); hideMenu.add(hideAllButSelection); viewMenu.add(newView); - if (!Jalview.isJS()) - { - viewMenu.add(expandViews); - viewMenu.add(gatherViews); - } + viewMenu.add(expandViews); + viewMenu.add(gatherViews); viewMenu.addSeparator(); viewMenu.add(showMenu); viewMenu.add(hideMenu); @@ -1830,7 +1858,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.addSeparator(); calculateMenu.add(expandAlignment); calculateMenu.add(extractScores); - if (!Jalview.isJS()) + if (!Platform.isJS()) { calculateMenu.addSeparator(); calculateMenu.add(runGroovy); @@ -1839,15 +1867,15 @@ public class GAlignFrame extends JInternalFrame webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); - if (!Jalview.isJS()) + if (!Platform.isJS()) { exportImageMenu.add(htmlMenuItem); } exportImageMenu.add(epsFile); exportImageMenu.add(createPNG); - exportImageMenu.add(createBioJS); - if (!Jalview.isJS()) + if (!Platform.isJS()) { + exportImageMenu.add(createBioJS); exportImageMenu.add(createSVG); } addSequenceMenu.add(addFromFile); @@ -1965,8 +1993,9 @@ public class GAlignFrame extends JInternalFrame } }); - annotationColour = new JMenuItem( + annotationColour = new JRadioButtonMenuItem( MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); annotationColour.addActionListener(new ActionListener() { @Override @@ -2352,15 +2381,15 @@ public class GAlignFrame extends JInternalFrame { } - protected void copy_actionPerformed(ActionEvent e) + protected void copy_actionPerformed() { } - protected void cut_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { } - protected void delete_actionPerformed(ActionEvent e) + protected void delete_actionPerformed() { } @@ -2462,7 +2491,7 @@ public class GAlignFrame extends JInternalFrame } - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { } @@ -2472,7 +2501,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }