X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=9de31aba717f37f2085d8b09f9af6dc25339cf3f;hb=07179fa211fc224a57afbb79f6e8239f36fbf6f0;hp=9f41c9224e61804d01d49fb043ee6aed58318337;hpb=2a7635954a40451d363a03e71393bf558413ef1e;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 9f41c92..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; @@ -62,15 +63,18 @@ 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(); @@ -78,7 +82,9 @@ public class GAlignFrame extends JInternalFrame protected JMenu sortByAnnotScore = new JMenu(); - protected JLabel statusBar = new JLabel(); + public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not + // sufficient for + // AlignFrame.printWriter protected JMenu outputTextboxMenu = new JMenu(); @@ -200,6 +206,8 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + protected JMenuItem openFeatureSettings; + private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; @@ -212,6 +220,10 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName(Jalview.getAppID("alignment")); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -225,7 +237,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); + outputText_actionPerformed(e.getActionCommand()); } }); @@ -236,7 +248,7 @@ 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'); @@ -260,7 +272,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); + saveAs_actionPerformed(); } }; @@ -533,7 +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")); @@ -544,7 +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 @@ -970,7 +986,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); @@ -983,7 +999,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -995,7 +1011,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1053,7 +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 @@ -1204,7 +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 @@ -1228,11 +1244,10 @@ public class GAlignFrame extends JInternalFrame /* * Translate as cDNA with sub-menu of translation tables */ - showTranslation.setText(MessageManager - .getString("label.translate_cDNA")); + 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); @@ -1299,7 +1314,7 @@ public class GAlignFrame extends JInternalFrame } }); - JMenuItem openFeatureSettings = new JMenuItem( + openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { @@ -1309,6 +1324,10 @@ 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() @@ -1316,7 +1335,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1330,7 +1349,8 @@ 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() { @@ -1343,7 +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 @@ -1357,7 +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 @@ -1724,7 +1745,10 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(webService); + if (!Platform.isJS()) + { + alignFrameMenuBar.add(webService); + } fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); @@ -1742,7 +1766,10 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); - fileMenu.add(loadVcf); + if (!Platform.isJS()) + { + fileMenu.add(loadVcf); + } fileMenu.addSeparator(); fileMenu.add(closeMenuItem); @@ -1837,17 +1864,26 @@ public class GAlignFrame extends JInternalFrame calculateMenu.addSeparator(); calculateMenu.add(expandAlignment); calculateMenu.add(extractScores); - calculateMenu.addSeparator(); - calculateMenu.add(runGroovy); + if (!Platform.isJS()) + { + calculateMenu.addSeparator(); + calculateMenu.add(runGroovy); + } webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); - exportImageMenu.add(htmlMenuItem); + if (!Platform.isJS()) + { + exportImageMenu.add(htmlMenuItem); + } exportImageMenu.add(epsFile); exportImageMenu.add(createPNG); - exportImageMenu.add(createBioJS); - exportImageMenu.add(createSVG); + if (!Platform.isJS()) + { + exportImageMenu.add(createBioJS); + exportImageMenu.add(createSVG); + } addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); @@ -2185,7 +2221,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String formatName) { } @@ -2351,15 +2387,15 @@ 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() { } @@ -2443,7 +2479,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void saveAs_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed() { } @@ -2471,7 +2507,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }