X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=0d6a03f3442af16edc02b5dd4c33e08b39518742;hb=adcef27f5747b4e70e89a56c3735bc3afb8ce9bf;hp=c228c9098f14590044c4a8c584acb4ad2b6c3e54;hpb=b5667f39acdf309cd92881b73edfda591e0acaf4;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index c228c90..0d6a03f 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(); } }; @@ -518,6 +529,26 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); + JMenuItem sortEValueMenuItem = new JMenuItem( + MessageManager.getString("action.by_evalue")); + sortEValueMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortEValueMenuItem_actionPerformed(e); + } + }); + JMenuItem sortBitScoreMenuItem = new JMenuItem( + MessageManager.getString("action.by_bit_score")); + sortBitScoreMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortBitScoreMenuItem_actionPerformed(e); + } + }); JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); @@ -532,6 +563,30 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); + + JMenuItem filterByEValue = new JMenuItem( + MessageManager.getString("action.filter_by_evalue")); + filterByEValue.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterByEValue_actionPerformed(); + } + + }); + + JMenuItem filterByScore = new JMenuItem( + MessageManager.getString("action.filter_by_score")); + filterByScore.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterByScore_actionPerformed(); + } + + }); JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( MessageManager.getString("action.pairwise_alignment")); @@ -987,7 +1042,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); @@ -1000,7 +1055,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -1012,7 +1067,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1258,8 +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()) @@ -1328,8 +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() { @@ -1339,6 +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() @@ -1346,7 +1405,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1367,7 +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() { @@ -1744,6 +1804,18 @@ public class GAlignFrame extends JInternalFrame selectHighlightedColumns_actionPerformed(actionEvent); } }; + JMenuItem Filter = new JMenuItem( + MessageManager.getString("action.select_highlighted_columns")); + selectHighlighted.setToolTipText( + MessageManager.getString("tooltip.select_highlighted_columns")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + selectHighlightedColumns_actionPerformed(actionEvent); + } + }; selectHighlighted.addActionListener(al); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); @@ -1762,7 +1834,10 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); - alignFrameMenuBar.add(hmmerMenu); + if (!Platform.isJS()) + { + alignFrameMenuBar.add(hmmerMenu); + } fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); @@ -1780,7 +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); @@ -1805,6 +1883,9 @@ public class GAlignFrame extends JInternalFrame // editMenu.add(justifyRightMenuItem); // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); + editMenu.addSeparator(); + editMenu.add(filterByEValue); + editMenu.add(filterByScore); showMenu.add(showAllColumns); showMenu.add(showAllSeqs); @@ -1860,6 +1941,8 @@ public class GAlignFrame extends JInternalFrame sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); + sort.add(sortEValueMenuItem); + sort.add(sortBitScoreMenuItem); sort.add(sortByTreeMenu); calculateMenu.add(sort); calculateMenu.add(calculateTree); @@ -1875,17 +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); @@ -2031,6 +2122,54 @@ public class GAlignFrame extends JInternalFrame // hmmSearch.add(addDatabase); /* + * jackhmmer + */ + JMenu jackhmmer = new JMenu( + MessageManager.getString("label.jackhmmer")); + JMenuItem jackhmmerSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + jackhmmerSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + jackhmmer_actionPerformed(false); + } + }); + JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "jackhmmer")); + jackhmmerRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + jackhmmer_actionPerformed(true); + } + + }); + /* + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + */ + jackhmmer.add(jackhmmerRun); + jackhmmer.add(jackhmmerSettings); + // hmmSearch.add(addDatabase); + + /* * top level menu */ hmmerMenu.setText(MessageManager.getString("action.hmmer")); @@ -2038,6 +2177,7 @@ public class GAlignFrame extends JInternalFrame hmmerMenu.add(hmmBuild); hmmerMenu.add(hmmAlign); hmmerMenu.add(hmmSearch); + hmmerMenu.add(jackhmmer); } @@ -2338,7 +2478,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String formatName) { } @@ -2456,6 +2596,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void sortEValueMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e) + { + } + protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { } @@ -2504,15 +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() { } @@ -2538,6 +2686,10 @@ public class GAlignFrame extends JInternalFrame { } + protected void jackhmmer_actionPerformed(boolean b) + { + } + protected void addDatabase_actionPerformed() throws FileFormatException, IOException { @@ -2603,6 +2755,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void filterByEValue_actionPerformed() + { + } + + protected void filterByScore_actionPerformed() + { + } + protected void scaleRight_actionPerformed(ActionEvent e) { } @@ -2615,7 +2775,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void saveAs_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed() { } @@ -2643,7 +2803,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { }