*/
package jalview.jbgui;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
-
-
@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
-
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
protected JMenuItem openFeatureSettings;
// for Web-page embedding using id=align-frame-div
setName(Platform.getAppID("alignment"));
-
jbInit();
setJMenuBar(alignFrameMenuBar);
private void jbInit() throws Exception
{
initColourMenu();
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
saveAs_actionPerformed();
}
};
+
// FIXME getDefaultToolkit throws an exception in Headless mode
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, Platform.SHORTCUT_KEY_MASK, false);
}
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
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,
}
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.deselect_all"));
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
}
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
JMenuItem grpsFromSelection = new JMenuItem(
MessageManager.getString("action.make_groups_selection"));
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
}
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
JMenuItem justifyLeftMenuItem = new JMenuItem(
MessageManager.getString("action.left_justify_alignment"));
sortGroupMenuItem_actionPerformed(e);
}
});
+
JMenuItem sortEValueMenuItem = new JMenuItem(
MessageManager.getString("action.by_evalue"));
sortEValueMenuItem.addActionListener(new ActionListener()
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
+
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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_actionPerformed(e);
}
});
+
JMenuItem createBioJS = new JMenuItem(
MessageManager.getString("label.biojs_html_export"));
bioJSMenuItem_actionPerformed(e);
}
});
+
JMenuItem overviewMenuItem = new JMenuItem(
MessageManager.getString("label.overview_window"));
overviewMenuItem_actionPerformed(e);
}
});
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
}
};
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"));
}
};
addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem_actionPerformed(e);
}
});
+
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
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);
}
+
});
.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
applyAutoAnnotationSettings_actionPerformed(e);
}
});
+
ButtonGroup buttonGroup = new ButtonGroup();
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
sortAnnotations_actionPerformed();
}
});
+
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
}
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
JMenuItem annotationColumn = new JMenuItem(
MessageManager.getString("action.select_by_annotation"));
annotationColumn_actionPerformed(e);
}
});
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
+
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
+
JMenuItem delete = new JMenuItem(
MessageManager.getString("action.delete"));
delete_actionPerformed();
}
});
+
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
}
};
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()
{
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
@Override
createEPS(null);
}
});
+
JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
createSVG(null);
}
});
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
loadTreeMenuItem_actionPerformed(e);
}
});
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
.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.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)
.setText(MessageManager.getString("action.calculate_tree_pca"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
showReverse_actionPerformed(true);
}
});
+
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
});
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(
fetchSequence_actionPerformed();
}
});
+
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
});
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
- autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
MessageManager.getString("label.sort_alignment_new_tree"));
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
- sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
listenToViewSelections_actionPerformed(e);
}
});
+
JMenu addSequenceMenu = new JMenu(
MessageManager.getString("label.add_sequences"));
hiddenMarkers_actionPerformed(e);
}
});
+
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
}
};
addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
showComplementMenuItem.setVisible(false);
showComplementMenuItem.addActionListener(new ActionListener()
showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
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,
}
};
addMenuActionAndAccelerator(keyStroke, save, al);
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload_actionPerformed(e);
}
});
+
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
}
};
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"));
}
};
addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
}
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
JMenuItem pageSetup = new JMenuItem(
MessageManager.getString("action.page_setup"));
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
{
alignFrameMenuBar.add(hmmerMenu);
}
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
}
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+
editMenu.addSeparator();
editMenu.add(filterByEValue);
editMenu.add(filterByScore);
viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
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();
protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
{
}
-
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
protected void hmmAlign_actionPerformed(boolean withDefaults)
{
}
-
public void createPNG(java.io.File f)
{
}
protected void filterByScore_actionPerformed()
{
}
-
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
{
}
-
}