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.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.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
protected JMenu hmmerMenu = new JMenu();
- protected JMenu hmmAlign = new JMenu();
-
- protected JMenuItem hmmAlignRun = new JMenuItem();
-
- protected JMenuItem hmmAlignSettings = new JMenuItem();
-
- protected JMenu hmmSearch = new JMenu();
-
- protected JMenuItem hmmSearchRun = new JMenuItem();
-
- protected JMenuItem hmmSearchSettings = new JMenuItem();
-
- protected JMenuItem addDatabase = new JMenuItem();
-
- protected JMenu hmmBuild = new JMenu();
-
- protected JMenuItem hmmBuildRun = new JMenuItem();
-
- protected JMenuItem hmmBuildSettings = new JMenuItem();
-
protected JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- public JLabel statusBar = new JLabel();
+ protected JLabel statusBar = new JLabel();
protected JMenu outputTextboxMenu = new JMenu();
protected JMenuItem modifyPID;
- protected JMenuItem annotationColour;
+ protected JRadioButtonMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu showTranslation = new JMenu();
protected JMenuItem showReverse = new JMenuItem();
private void jbInit() throws Exception
{
initColourMenu();
- initHMMERMenu();
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
- hmmerMenu.setText(MessageManager.getString("action.hmmer"));
- hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
- hmmerMenu.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmerMenu_actionPerformed(e);
- }
- });
- hmmerMenu.add(hmmBuild);
- hmmerMenu.add(hmmAlign);
- hmmerMenu.add(hmmSearch);
+
+ initHMMERMenu();
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), 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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), 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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
vamsasStore_actionPerformed(e);
}
});
- showTranslation
- .setText(MessageManager.getString("label.translate_cDNA"));
- showTranslation.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+
+ /*
+ * Translate as cDNA with sub-menu of translation tables
+ */
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
+ boolean first = true;
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
+ {
+ JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+ showTranslation.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(table);
+ }
+ });
+ if (first)
{
- showTranslation_actionPerformed(e);
+ showTranslation.addSeparator();
}
- });
+ first = false;
+ }
+
showReverse.setText(MessageManager.getString("label.reverse"));
showReverse.addActionListener(new ActionListener()
{
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
- hmmBuildRun.setText(MessageManager.formatMessage(
- "label.action_with_default_settings", "hmmbuild"));
- hmmBuildRun.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmBuildRun_actionPerformed();
- }
- });
- hmmBuildSettings.setText(
- MessageManager.getString("label.edit_settings_and_run"));
- hmmBuildSettings.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmBuildSettings_actionPerformed();
- }
- });
- hmmAlignRun.setText(MessageManager.formatMessage(
- "label.action_with_default_settings", "hmmalign"));
- hmmAlignRun.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmAlignRun_actionPerformed();
- }
- });
- hmmAlignSettings.setText(
- MessageManager.getString("label.edit_settings_and_run"));
- hmmAlignSettings.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmAlignSettings_actionPerformed();
- }
- });
- hmmSearchRun.setText(MessageManager.formatMessage(
- "label.action_with_default_settings", "hmmsearch"));
- hmmSearchRun.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmSearchRun_actionPerformed();
- }
- });
- addDatabase.setText(MessageManager.getString("label.add_database"));
- addDatabase.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- addDatabase_actionPerformed();
- } catch (IOException e1)
- {
- e1.printStackTrace();
- }
- }
- });
- hmmSearchSettings.setText(
- MessageManager.getString("label.edit_settings_and_run"));
- hmmSearchSettings.addActionListener(new ActionListener()
+ 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 e)
+ public void actionPerformed(ActionEvent actionEvent)
{
- hmmSearchSettings_actionPerformed();
+ selectHighlightedColumns_actionPerformed(actionEvent);
}
- });
+ };
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
// selectMenu.add(listenToViewSelections);
}
- public void hmmerMenu_actionPerformed(ActionEvent e)
- {
-
- }
-
/**
- * Constructs the entries on the HMMER menu (does not add them to the menu).
+ * Constructs the entries on the HMMER menu
*/
protected void initHMMERMenu()
{
- hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
- hmmAlignSettings = new JMenuItem(
- MessageManager.getString("label.edit_settings_and_run"));
- hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
- "label.action_with_default_settings", "hmmalign"));
- hmmAlign.add(hmmAlignSettings);
- hmmAlign.add(hmmAlignRun);
- hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
- hmmBuildSettings = new JMenuItem(
+ /*
+ * hmmbuild
+ */
+ JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ JMenuItem hmmBuildSettings = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+ hmmBuildSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
"label.action_with_default_settings", "hmmbuild"));
- hmmBuild.add(hmmBuildSettings);
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(true);
+ }
+ });
hmmBuild.add(hmmBuildRun);
- hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
- hmmSearchSettings = new JMenuItem(
+ hmmBuild.add(hmmBuildSettings);
+
+ /*
+ * hmmalign
+ */
+ JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+ JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlignRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(true);
+ }
+ });
+ JMenuItem hmmAlignSettings = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+ hmmAlignSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(false);
+ }
+ });
+ hmmAlign.add(hmmAlignRun);
+ hmmAlign.add(hmmAlignSettings);
+
+ /*
+ * hmmsearch
+ */
+ JMenu hmmSearch = new JMenu(
+ MessageManager.getString("label.hmmsearch"));
+ JMenuItem hmmSearchSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
"label.action_with_default_settings", "hmmsearch"));
- addDatabase = new JMenuItem(
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(true);
+ }
+ });
+ JMenuItem addDatabase = new JMenuItem(
MessageManager.getString("label.add_database"));
- hmmSearch.add(hmmSearchSettings);
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
hmmSearch.add(hmmSearchRun);
- hmmSearch.add(addDatabase);
+ hmmSearch.add(hmmSearchSettings);
+ // 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.setEnabled(HmmerCommand.isHmmerAvailable());
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+ hmmerMenu.add(jackhmmer);
+
}
protected void loadVcf_actionPerformed()
}
});
- annotationColour = new JMenuItem(
+ annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
annotationColour.addActionListener(new ActionListener()
{
@Override
{
}
- protected void hmmBuildRun_actionPerformed()
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
{
}
- protected void hmmSearchRun_actionPerformed()
- {
- }
-
- protected void addDatabase_actionPerformed()
- throws FileFormatException, IOException
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
{
}
- protected void hmmAlignRun_actionPerformed()
+ protected void jackhmmer_actionPerformed(boolean b)
{
}
- protected void hmmBuildSettings_actionPerformed()
- {
- }
-
- protected void hmmSearchSettings_actionPerformed()
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
{
}
- protected void hmmAlignSettings_actionPerformed()
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
{
}
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
-
- protected void showInformationHistogram_actionPerformed(ActionEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
-
- }
}
git://source.jalview.org / jalview.git / blobdiff