X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=38ad43795f322171214e3cb85adf4713b619e93d;hb=ae737f35e5185aa421563e4c061340a3c4152514;hp=7a85a4a7074b150b42aae1a524bfa05d32a2dab4;hpb=c84b1b8d4704cb7891c45ba6219cb6e7c09cca91;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 7a85a4a..38ad437 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,26 +21,34 @@ 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.gui.JvSwingUtils; +import jalview.gui.PaintRefresher; import jalview.gui.Preferences; +import jalview.gui.TreePanel; import jalview.io.FileFormats; +import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Component; import java.awt.GridLayout; -import java.awt.Toolkit; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; +import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.util.ArrayList; import java.util.HashMap; +import java.util.List; import java.util.Map; import javax.swing.BorderFactory; @@ -59,15 +67,18 @@ 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(); @@ -75,7 +86,9 @@ 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(); @@ -123,7 +136,7 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem modifyPID; - protected JMenuItem annotationColour; + protected JRadioButtonMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); @@ -137,7 +150,7 @@ 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(); @@ -196,14 +209,14 @@ 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; @@ -211,6 +224,11 @@ public class GAlignFrame extends JInternalFrame { try { + + // for Web-page embedding using id=align-frame-div + setName(Platform.getAppID("alignment")); + + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -224,7 +242,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); + outputText_actionPerformed(e.getActionCommand()); } }); @@ -235,7 +253,7 @@ 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'); @@ -259,20 +277,17 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); + saveAs_actionPerformed(); } }; // FIXME getDefaultToolkit throws an exception in Headless mode - KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, + KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK, false); addMenuActionAndAccelerator(keyStroke, saveAs, al); closeMenuItem.setText(MessageManager.getString("action.close")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -284,16 +299,7 @@ public class GAlignFrame extends JInternalFrame addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); - JMenu viewMenu = new JMenu(MessageManager.getString("action.view")) { - - public void setPopupMenuVisible(boolean b) { - if (b) { - openFeatureSettings.setEnabled(haveAlignmentFeatures()); - } - super.setPopupMenuVisible(b); - } - - }; + JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); JMenu annotationsMenu = new JMenu( MessageManager.getString("action.annotations")); JMenu showMenu = new JMenu(MessageManager.getString("action.show")); @@ -304,7 +310,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem selectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.select_all")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -331,7 +337,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem invertSequenceMenuItem = new JMenuItem( MessageManager.getString("action.invert_sequence_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -367,7 +373,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem remove2LeftMenuItem = new JMenuItem( MessageManager.getString("action.remove_left")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -381,7 +387,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem remove2RightMenuItem = new JMenuItem( MessageManager.getString("action.remove_right")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -395,7 +401,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeGappedColumnMenuItem = new JMenuItem( MessageManager.getString("action.remove_empty_columns")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -409,8 +415,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeAllGapsMenuItem = new JMenuItem( MessageManager.getString("action.remove_all_gaps")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -517,7 +523,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -692,7 +698,7 @@ public class GAlignFrame extends JInternalFrame undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -706,7 +712,7 @@ public class GAlignFrame extends JInternalFrame redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -730,7 +736,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -756,7 +762,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); al = new ActionListener() @@ -917,7 +923,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -942,7 +948,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem createGroup = new JMenuItem( MessageManager.getString("action.create_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -956,8 +962,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem unGroup = new JMenuItem( MessageManager.getString("action.remove_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -971,27 +977,27 @@ public class GAlignFrame extends JInternalFrame copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + copy_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, copy, al); cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + cut_actionPerformed(); } }; addMenuActionAndAccelerator(keyStroke, cut, al); @@ -1003,7 +1009,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + delete_actionPerformed(); } }); @@ -1011,8 +1017,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem pasteNew = new JMenuItem( MessageManager.getString("label.to_new_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -1027,7 +1033,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem pasteThis = new JMenuItem( MessageManager.getString("label.to_this_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1170,6 +1176,24 @@ public class GAlignFrame extends JInternalFrame @Override public void menuSelected(MenuEvent e) { + enableSortMenuOptions(); + } + + @Override + public void menuDeselected(MenuEvent e) + { + } + + @Override + public void menuCanceled(MenuEvent e) + { + } + }); + sortByTreeMenu.addMenuListener(new MenuListener() + { + @Override + public void menuSelected(MenuEvent e) + { buildTreeSortMenu(); } @@ -1232,16 +1256,33 @@ 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.getInstance() + .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() { @@ -1292,7 +1333,6 @@ public class GAlignFrame extends JInternalFrame openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); - openFeatureSettings.setEnabled(false); openFeatureSettings.addActionListener(new ActionListener() { @Override @@ -1301,6 +1341,10 @@ 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() @@ -1308,7 +1352,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fetchSequence_actionPerformed(e); + fetchSequence_actionPerformed(); } }); @@ -1322,7 +1366,8 @@ 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() { @@ -1523,8 +1568,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem invertColSel = new JMenuItem( MessageManager.getString("action.invert_column_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.ALT_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.ALT_DOWN_MASK, false); al = new ActionListener() { @@ -1587,7 +1632,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1612,7 +1657,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem newView = new JMenuItem( MessageManager.getString("action.new_view")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1689,8 +1734,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem selectHighlighted = new JMenuItem( MessageManager.getString("action.select_highlighted_columns")); - selectHighlighted.setToolTipText( - MessageManager.getString("tooltip.select_highlighted_columns")); + selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("tooltip.select_highlighted_columns"))); al = new ActionListener() { @Override @@ -1716,7 +1761,10 @@ 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); @@ -1734,10 +1782,7 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); - /* - * No VCF import in Jalview-JS - * @j2sNative - */ + if (!Platform.isJS()) { fileMenu.add(loadVcf); } @@ -1835,17 +1880,26 @@ 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); @@ -1886,12 +1940,10 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } - protected boolean haveAlignmentFeatures() + protected void enableSortMenuOptions() { - // because gAlignFrame is not an abstract class -- see AlignFrame - return false; } - + protected void loadVcf_actionPerformed() { } @@ -1967,8 +2019,9 @@ 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 @@ -2188,7 +2241,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String formatName) { } @@ -2354,15 +2407,15 @@ 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() { } @@ -2446,7 +2499,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void saveAs_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed() { } @@ -2464,7 +2517,7 @@ public class GAlignFrame extends JInternalFrame } - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { } @@ -2474,7 +2527,7 @@ public class GAlignFrame extends JInternalFrame } - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { } @@ -2689,4 +2742,6 @@ public class GAlignFrame extends JInternalFrame protected void showComplement_actionPerformed(boolean complement) { } + + }