X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=9de31aba717f37f2085d8b09f9af6dc25339cf3f;hb=d55521c4db0fb537c343a28ce2294abf021eea3a;hp=342d95a8466147ee41718f1f9205a242b2a35573;hpb=d61781b1fdb2e634445ee02f3718f81673af96ac;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 342d95a..9de31ab 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,12 +21,15 @@ 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; @@ -60,15 +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(); @@ -76,7 +82,9 @@ 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 +132,7 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem modifyPID; - protected JMenuItem annotationColour; + protected JRadioButtonMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); @@ -138,7 +146,7 @@ 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 +178,7 @@ 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 +205,14 @@ 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 +220,10 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName(Jalview.getAppID("alignment")); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -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'); @@ -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 @@ -1224,16 +1240,32 @@ 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.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() { @@ -1292,6 +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() @@ -1299,7 +1335,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1313,7 +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() { @@ -1326,7 +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 @@ -1340,7 +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 @@ -1707,7 +1745,7 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - if (!Jalview.isJS()) + if (!Platform.isJS()) { alignFrameMenuBar.add(webService); } @@ -1728,7 +1766,7 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); - if (!Jalview.isJS()) + if (!Platform.isJS()) { fileMenu.add(loadVcf); } @@ -1826,7 +1864,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.addSeparator(); calculateMenu.add(expandAlignment); calculateMenu.add(extractScores); - if (!Jalview.isJS()) + if (!Platform.isJS()) { calculateMenu.addSeparator(); calculateMenu.add(runGroovy); @@ -1835,15 +1873,15 @@ 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); @@ -1961,8 +1999,9 @@ 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 @@ -2348,15 +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() { } @@ -2458,7 +2497,7 @@ public class GAlignFrame extends JInternalFrame } - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { } @@ -2468,7 +2507,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }