*/
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.Preferences;
-import jalview.hmmer.HmmerCommand;
-import jalview.io.FileFormatException;
-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.GridLayout;
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 javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+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.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+
+@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu webService = new JMenu();
-
- protected JMenu hmmerMenu = 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 JMenuItem webServiceNoServices;
+ public JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JMenuItem openFeatureSettings;
+
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName(Platform.getAppID("alignment"));
+
+
jbInit();
setJMenuBar(alignFrameMenuBar);
@Override
public void actionPerformed(ActionEvent e)
{
- outputText_actionPerformed(e);
+ outputText_actionPerformed(e.getActionCommand());
}
});
System.err.println(e.toString());
}
- if (!Platform.isAMac())
+ if (Platform.allowMnemonics()) // was "not mac and not JS"
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
@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,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_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,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
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"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
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"));
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), 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,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ cut_actionPerformed();
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
@Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ delete_actionPerformed();
}
});
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
@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();
}
/*
* 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())
runGroovy_actionPerformed();
}
});
-
- JMenuItem openFeatureSettings = new JMenuItem(
+
+ openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
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()
@Override
public void actionPerformed(ActionEvent e)
{
- fetchSequence_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
}
}
});
- 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()
{
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.ALT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
});
JMenuItem selectHighlighted = new JMenuItem(
MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("tooltip.select_highlighted_columns")));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
+ JMenuItem Filter = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
selectHighlighted.setToolTipText(
MessageManager.getString("tooltip.select_highlighted_columns"));
al = new ActionListener()
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
- alignFrameMenuBar.add(hmmerMenu);
+ if (!Platform.isJS())
+ {
+ alignFrameMenuBar.add(hmmerMenu);
+ }
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
- fileMenu.add(loadVcf);
+ if (!Platform.isJS())
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
+ sort.add(sortEValueMenuItem);
+ sort.add(sortBitScoreMenuItem);
sort.add(sortByTreeMenu);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
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);
// 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"));
hmmerMenu.add(hmmBuild);
hmmerMenu.add(hmmAlign);
hmmerMenu.add(hmmSearch);
+ hmmerMenu.add(jackhmmer);
}
+ protected void enableSortMenuOptions()
+ {
+ }
+
protected void loadVcf_actionPerformed()
{
}
{
}
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
{
}
+ protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
{
}
- 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()
{
}
{
}
+ protected void jackhmmer_actionPerformed(boolean b)
+ {
+ }
+
protected void addDatabase_actionPerformed()
throws FileFormatException, IOException
{
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
{
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed()
{
}
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
+
+
}