X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6148d865a1f5d716924aa3ab437f5932dd7adad3;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=579da08af93b7079751411284f6aac887fca1786;hpb=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 579da08..6148d86 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -64,17 +64,20 @@ 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 + // JBP - followed suite for these other service related GUI elements. + // TODO: check we really need these to be public + public JMenu hmmerMenu = new JMenu(); - protected JMenu hmmerMenu = new JMenu(); - - protected JMenuItem webServiceNoServices; + public JMenuItem webServiceNoServices; protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); @@ -82,7 +85,9 @@ 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(); @@ -210,6 +215,8 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + protected JMenuItem openFeatureSettings; + private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; @@ -222,6 +229,10 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName("jalview-alignment"); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -235,7 +246,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); + outputText_actionPerformed(e.getActionCommand()); } }); @@ -246,7 +257,7 @@ 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'); @@ -270,7 +281,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); + saveAs_actionPerformed(); } }; @@ -1031,7 +1042,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); @@ -1044,7 +1055,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -1056,7 +1067,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1302,8 +1313,8 @@ 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()) @@ -1372,8 +1383,8 @@ public class GAlignFrame extends JInternalFrame runGroovy_actionPerformed(); } }); - - JMenuItem openFeatureSettings = new JMenuItem( + + openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { @@ -1383,6 +1394,10 @@ 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() @@ -1390,7 +1405,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1411,7 +1426,8 @@ public class GAlignFrame extends JInternalFrame } } }); - 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() { @@ -1817,8 +1833,11 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(webService); - alignFrameMenuBar.add(hmmerMenu); + if (!Platform.isJS()) + { + alignFrameMenuBar.add(webService); + alignFrameMenuBar.add(hmmerMenu); + } fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); @@ -1836,7 +1855,10 @@ 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); @@ -1936,17 +1958,25 @@ 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); @@ -2448,7 +2478,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String formatName) { } @@ -2622,15 +2652,15 @@ 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() { } @@ -2745,7 +2775,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void saveAs_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed() { } @@ -2773,7 +2803,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }