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 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;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
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 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 hiddenMarkers = new JCheckBoxMenuItem();
- protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
+ protected JTabbedPane tabbedPane = new JTabbedPane();
protected JMenuItem reload = new JMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
-
+
protected JMenuItem openFeatureSettings;
private SequenceAnnotationOrder annotationSortOrder;
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName("jalview-alignment");
+
jbInit();
setJMenuBar(alignFrameMenuBar);
private void jbInit() throws Exception
{
initColourMenu();
-
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed();
}
};
-
+
// 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
}
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
JMenu annotationsMenu = new JMenu(
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+
+ 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
}
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+
JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.deselect_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+
JMenuItem grpsFromSelection = new JMenuItem(
MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new ActionListener()
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
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+
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()
{
}
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+
JMenuItem justifyLeftMenuItem = new JMenuItem(
MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem.addActionListener(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,
- 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"));
pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
-
+
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
+
outputTextboxMenu
.setText(MessageManager.getString("label.out_to_textbox"));
+
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
+
sortAnnBySequence.setSelected(
sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
colourTextMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem htmlMenuItem = new JMenuItem(
MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new ActionListener()
htmlMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem createBioJS = new JMenuItem(
MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
bioJSMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem overviewMenuItem = new JMenuItem(
MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new ActionListener()
overviewMenuItem_actionPerformed(e);
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
wrapMenuItem_actionPerformed(e);
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem_actionPerformed(e);
}
});
-
+
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()
showSeqFeatures.setText(
MessageManager.getString("label.show_sequence_features"));
+
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
.setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
showNpFeatsMenuitem.setText(
MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
showGroupConservation
.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
showGroupConsensus
.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
showConsensusHistogram.setText(
MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
});
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
-
+
});
normaliseSequenceLogo
.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
applyAutoAnnotationSettings
.setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings_actionPerformed(e);
}
});
-
+
ButtonGroup buttonGroup = new ButtonGroup();
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
MessageManager.getString("label.show_first"));
sortAnnotations_actionPerformed();
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+
JMenuItem annotationColumn = new JMenuItem(
MessageManager.getString("action.select_by_annotation"));
annotationColumn.addActionListener(new ActionListener()
annotationColumn_actionPerformed(e);
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+
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()
{
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
-
+
JMenuItem delete = new JMenuItem(
MessageManager.getString("action.delete"));
delete.addActionListener(new ActionListener()
delete_actionPerformed();
}
});
-
+
pasteMenu.setText(MessageManager.getString("action.paste"));
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()
{
@Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ try
+ {
+ pasteNew_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+
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
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ try
+ {
+ pasteThis_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
});
createPNG.setActionCommand(
MessageManager.getString("label.save_png_image"));
-
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
createEPS(null);
}
});
-
+
JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
{
createSVG(null);
}
});
-
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
loadTreeMenuItem.setActionCommand(
loadTreeMenuItem_actionPerformed(e);
}
});
-
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new ActionListener()
.setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
}
-
+
});
-
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
{
buildTreeSortMenu();
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuCanceled(MenuEvent e)
{
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
-
+
@Override
public void menuCanceled(MenuEvent e)
{
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuSelected(MenuEvent e)
{
/*
* 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())
showReverse_actionPerformed(true);
}
});
-
+
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
extractScores.addActionListener(new ActionListener()
});
extractScores.setVisible(true);
// JBPNote: TODO: make gui for regex based score extraction
-
+
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+
runGroovy.setText(MessageManager.getString("label.run_groovy"));
runGroovy.setToolTipText(
MessageManager.getString("label.run_groovy_tip"));
fetchSequence_actionPerformed();
}
});
-
+
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ try
+ {
+ associatedData_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
- 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()
{
listenToViewSelections_actionPerformed(e);
}
});
-
+
JMenu addSequenceMenu = new JMenu(
MessageManager.getString("label.add_sequences"));
JMenuItem addFromFile = new JMenuItem(
hiddenMarkers_actionPerformed(e);
}
});
-
+
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()
{
}
};
addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+
showComplementMenuItem.setVisible(false);
showComplementMenuItem.addActionListener(new ActionListener()
{
showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
-
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_mousePressed(e);
}
}
-
+
@Override
public void mouseReleased(MouseEvent e)
{
tabbedPane_focusGained(e);
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, save, al);
-
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
-
+
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
}
};
addMenuActionAndAccelerator(keyStroke, newView, al);
-
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
-
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign_actionPerformed(e);
}
});
-
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+
JMenuItem pageSetup = new JMenuItem(
MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
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"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(webService);
if (!Platform.isJS())
{
- alignFrameMenuBar.add(webService);
+ alignFrameMenuBar.add(hmmerMenu);
}
-
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
}
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
-
+
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
-
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
+
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
showMenu.add(showAllhidden);
viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
-
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAllAlAnnotations);
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(runGroovy);
}
-
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
// selectMenu.add(listenToViewSelections);
}
+ /**
+ * Constructs the entries on the HMMER menu
+ */
+ protected void initHMMERMenu()
+ {
+ /*
+ * hmmbuild
+ */
+ JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ JMenuItem hmmBuildSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ 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"));
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(true);
+ }
+ });
+ hmmBuild.add(hmmBuildRun);
+ 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"));
+ 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"));
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_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();
+ }
+ }
+ });
+ hmmSearch.add(hmmSearchRun);
+ 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()
{
}
{
}
+ protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
}
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
{
}
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void jackhmmer_actionPerformed(boolean b)
+ {
+ }
+
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
+ {
+ }
+
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ }
+
public void createPNG(java.io.File f)
{
}
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
}
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
git://source.jalview.org / jalview.git / blobdiff