X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=8bbfb8d10d23cbf2511c6600d831ef7fc4e9ea3a;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=0ee03bc84fde7d42a85c03679c211a9fc268a571;hpb=8956fdfd008d0d949814c4680a7b3a55969e39e1;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 0ee03bc..8bbfb8d 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -28,6 +28,7 @@ import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; import jalview.io.FileFormats; +import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; import jalview.util.Platform; @@ -61,15 +62,18 @@ 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(); @@ -77,7 +81,9 @@ 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(); @@ -125,7 +131,7 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem modifyPID; - protected JMenuItem annotationColour; + protected JRadioButtonMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); @@ -199,6 +205,8 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + protected JMenuItem openFeatureSettings; + private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; @@ -211,6 +219,10 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName("jalview-alignment"); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -224,7 +236,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); + outputText_actionPerformed(e.getActionCommand()); } }); @@ -235,7 +247,7 @@ 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'); @@ -259,7 +271,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); + saveAs_actionPerformed(); } }; @@ -969,7 +981,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); @@ -982,7 +994,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -994,7 +1006,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1227,8 +1239,8 @@ 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()) @@ -1298,7 +1310,7 @@ public class GAlignFrame extends JInternalFrame } }); - JMenuItem openFeatureSettings = new JMenuItem( + openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { @@ -1308,6 +1320,10 @@ 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() @@ -1315,7 +1331,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1329,7 +1345,8 @@ 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() { @@ -1723,7 +1740,10 @@ 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); @@ -1741,7 +1761,10 @@ 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); @@ -1836,17 +1859,26 @@ 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); @@ -1962,8 +1994,9 @@ 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 @@ -2183,7 +2216,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String formatName) { } @@ -2349,15 +2382,15 @@ 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() { } @@ -2441,7 +2474,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void saveAs_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed() { } @@ -2469,7 +2502,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }