*/
package jalview.jbgui;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JTabbedPane;
+import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.MenuEvent;
protected JMenu viewMenu = new JMenu();
+ protected JMenu annotationsMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
JMenuItem createPNG = new JMenuItem();
+ JMenuItem createBioJS = new JMenuItem();
+
+ JMenuItem createSVG = new JMenuItem();
+
protected JMenuItem font = new JMenuItem();
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu cdna = new JMenu();
+
protected JMenuItem extractScores = new JMenuItem();
protected JMenuItem expandAlignment = new JMenuItem();
JMenuItem annotationColour = new JMenuItem();
+ JMenuItem annotationColumn = new JMenuItem();
+
protected JMenuItem rnahelicesColour = new JMenuItem();
JMenuItem associatedData = new JMenuItem();
JMenuItem showAllhidden = new JMenuItem();
- protected JMenuItem showAllAnnotations = new JMenuItem();
+ protected JMenuItem showAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAlAnnotations = new JMenuItem();
- protected JMenuItem hideAllAnnotations = new JMenuItem();
+ protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
JMenuItem textColour = new JMenuItem();
- JMenu formatMenu = new JMenu();
+ protected JMenu formatMenu = new JMenu();
JMenu selectMenu = new JMenu();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
+
private JMenuItem grpsFromSelection = new JMenuItem();
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
public GAlignFrame()
{
try
JMenuItem item = new JMenuItem(
jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
private void jbInit() throws Exception
{
fileMenu.setText(MessageManager.getString("action.file"));
+
saveAs.setText(MessageManager.getString("action.save_as") + "...");
- saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- saveAs.addActionListener(new ActionListener()
+ ActionListener al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
saveAs_actionPerformed(e);
}
- });
+ };
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
closeMenuItem.setText(MessageManager.getString("action.close"));
- closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
closeMenuItem_actionPerformed(false);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
editMenu.setText(MessageManager.getString("action.edit"));
viewMenu.setText(MessageManager.getString("action.view"));
+ annotationsMenu.setText(MessageManager.getString("action.annotations"));
colourMenu.setText(MessageManager.getString("action.colour"));
calculateMenu.setText(MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+
selectAllSequenceMenuItem.setText(MessageManager
.getString("action.select_all"));
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- selectAllSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- selectAllSequenceMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
deselectAllSequenceMenuItem.setText(MessageManager
.getString("action.deselect_all"));
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- deselectAllSequenceMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
invertSequenceMenuItem.setText(MessageManager
.getString("action.invert_sequence_selection"));
- invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- invertSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- invertSequenceMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
grpsFromSelection.setText(MessageManager
.getString("action.make_groups_selection"));
- grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ grpsFromSelection.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
.getString("action.view_flanking_regions"));
expandAlignment.setToolTipText(MessageManager
.getString("label.view_flanking_regions"));
- expandAlignment.addActionListener(new java.awt.event.ActionListener()
+ expandAlignment.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
remove2LeftMenuItem.setText(MessageManager
.getString("action.remove_left"));
- remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- remove2LeftMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2LeftMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
remove2RightMenuItem.setText(MessageManager
.getString("action.remove_right"));
- remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- remove2RightMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2RightMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
removeGappedColumnMenuItem.setText(MessageManager
.getString("action.remove_empty_columns"));
- removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeGappedColumnMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeGappedColumnMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
removeAllGapsMenuItem.setText(MessageManager
.getString("action.remove_all_gaps"));
- removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- removeAllGapsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeAllGapsMenuItem_actionPerformed(e);
- }
- });
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
justifyLeftMenuItem.setText(MessageManager
.getString("action.left_justify_alignment"));
- justifyLeftMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyLeftMenuItem_actionPerformed(e);
- }
- });
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
justifyRightMenuItem.setText(MessageManager
.getString("action.right_justify_alignment"));
- justifyRightMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyRightMenuItem_actionPerformed(e);
- }
- });
+ justifyRightMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
viewTextMenuItem.setText(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
showNonconservedMenuItem.setText(MessageManager
.getString("label.show_non_conversed"));
showNonconservedMenuItem.setState(false);
- showNonconservedMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- showUnconservedMenuItem_actionPerformed(e);
- }
- });
+ showNonconservedMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
sortPairwiseMenuItem.setText(MessageManager
.getString("action.by_pairwise_id"));
- sortPairwiseMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortPairwiseMenuItem_actionPerformed(e);
- }
- });
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortIDMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
sortLengthMenuItem
.setText(MessageManager.getString("action.by_length"));
- sortLengthMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortLengthMenuItem_actionPerformed(e);
- }
- });
+ sortLengthMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText(MessageManager
- .getString("action.remove_redundancy").concat("..."));
- removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeRedundancyMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeRedundancyMenuItem_actionPerformed(e);
- }
- });
+
+ removeRedundancyMenuItem.setText(MessageManager.getString(
+ "action.remove_redundancy").concat("..."));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
pairwiseAlignmentMenuItem.setText(MessageManager
.getString("action.pairwise_alignment"));
- pairwiseAlignmentMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- pairwiseAlignmentMenuItem_actionPerformed(e);
- }
- });
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
PCAMenuItem.setText(MessageManager
.getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ PCAMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
averageDistanceTreeMenuItem.setText(MessageManager
.getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
+ averageDistanceTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
neighbourTreeMenuItem.setText(MessageManager
.getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
+ neighbourTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
.getString("label.out_to_textbox"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ clustalColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ zappoColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
hydrophobicityColour.setText(MessageManager
.getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
+ hydrophobicityColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ helixColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
strandColour.setText(MessageManager
.getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ strandColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ turnColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
userDefinedColour.setText(MessageManager
.getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
PIDColour
.setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ PIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
BLOSUM62Colour
.setText(MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ nucleotideColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
purinePyrimidineColour.setText(MessageManager
.getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed(e);
- }
- });
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed(e);
- }
- });
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(e); } });
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
+ * });
*/
avDistanceTreeBlosumMenuItem.setText(MessageManager
.getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
+ avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
njTreeBlosumMenuItem.setText(MessageManager
.getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
+ njTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText(MessageManager
.getString("label.show_annotations"));
annotationPanelMenuItem_actionPerformed(e);
}
});
- /*
- * Show/hide all annotations only enabled if annotation panel is shown
- */
- showAllAnnotations.setText(MessageManager
- .getString("label.show_all_annotations"));
- showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
- showAllAnnotations.addActionListener(new ActionListener()
+ showAllAlAnnotations.setText(MessageManager
+ .getString("label.show_all_al_annotations"));
+ final boolean isAnnotationPanelShown = annotationPanelMenuItem
+ .getState();
+ showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllAlAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ hideAllAlAnnotations.setText(MessageManager
+ .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllAlAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ showAllSeqAnnotations.setText(MessageManager
+ .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllSeqAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- showAllAnnotations_actionPerformed();
+ showAllAnnotations_actionPerformed(true, false);
}
});
- hideAllAnnotations.setText(MessageManager
- .getString("label.hide_all_annotations"));
- hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAnnotations.addActionListener(new ActionListener()
+ hideAllSeqAnnotations.setText(MessageManager
+ .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllSeqAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- hideAllAnnotations_actionPerformed();
+ hideAllAnnotations_actionPerformed(true, false);
+ }
+ });
+ SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBySequence.setText(MessageManager
+ .getString("label.sort_annotations_by_sequence"));
+ sortAnnBySequence
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
+ }
+ });
+ sortAnnByLabel.setText(MessageManager
+ .getString("label.sort_annotations_by_label"));
+ sortAnnByLabel
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
colourTextMenuItem.setText(MessageManager
.getString("label.colour_text"));
- colourTextMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- colourTextMenuItem_actionPerformed(e);
- }
- });
+ colourTextMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
htmlMenuItem.setText(MessageManager.getString("label.html"));
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ htmlMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
htmlMenuItem_actionPerformed(e);
}
});
+
+ // TODO uncomment when supported by MassageManager
+ // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
+ createBioJS.setText("BioJS");
+ createBioJS.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ bioJSMenuItem_actionPerformed(e);
+ }
+ });
+
overviewMenuItem.setText(MessageManager
.getString("label.overview_window"));
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ overviewMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
overviewMenuItem_actionPerformed(e);
}
});
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
undoMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
conservationMenuItem.setText(MessageManager
.getString("action.by_conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ noColourmenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
wrapMenuItem_actionPerformed(e);
}
});
+
printMenuItem.setText(MessageManager.getString("action.print") + "...");
- printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
printMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
- renderGapsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_actionPerformed(e);
- }
- });
+ renderGapsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+
findMenuItem.setText(MessageManager.getString("action.find"));
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- findMenuItem.setToolTipText(MessageManager.getString("label.find_tip"));
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
findMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
abovePIDThreshold.setText(MessageManager
.getString("label.above_identity_threshold"));
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ abovePIDThreshold.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
}
+ });
+ ButtonGroup buttonGroup = new ButtonGroup();
+ buttonGroup.add(showAutoFirst);
+ buttonGroup.add(showAutoLast);
+ showAutoFirst.setText(MessageManager.getString("label.show_first"));
+ showAutoFirst.setSelected(Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false));
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setText(MessageManager.getString("label.show_last"));
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ nucleotideColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
deleteGroups
.setText(MessageManager.getString("action.undefine_groups"));
- deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
deleteGroups_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
createGroup.setText(MessageManager.getString("action.create_groups"));
- createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- createGroup.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
createGroup_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
unGroup.setText(MessageManager.getString("action.remove_group"));
- unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- unGroup.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
unGroup_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
copy.setText(MessageManager.getString("action.copy"));
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
- copy.addActionListener(new java.awt.event.ActionListener()
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
cut.setText(MessageManager.getString("action.cut"));
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- cut.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
delete.setText(MessageManager.getString("action.delete"));
- delete.addActionListener(new java.awt.event.ActionListener()
+ delete.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
delete_actionPerformed(e);
}
});
+
pasteMenu.setText(MessageManager.getString("action.paste"));
pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- pasteNew.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
pasteNew_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
- pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- pasteThis.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
pasteThis_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
applyToAllGroups.setText(MessageManager
.getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ applyToAllGroups.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
applyToAllGroups_actionPerformed(e);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+ createPNG.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
createPNG.setActionCommand(MessageManager
.getString("label.save_png_image"));
createPNG.setText("PNG");
+
font.setText(MessageManager.getString("action.font"));
- font.addActionListener(new java.awt.event.ActionListener()
+ font.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
-
seqLimits.setText(MessageManager
.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
- seqLimits.addActionListener(new java.awt.event.ActionListener()
+ seqLimits.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
epsFile.setText("EPS");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+ epsFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
createEPS(null);
}
});
+
+ createSVG.setText("SVG");
+ createSVG.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSVG(null);
+ }
+ });
+
LoadtreeMenuItem.setActionCommand(MessageManager
.getString("label.load_tree_for_sequence_set"));
LoadtreeMenuItem.setText(MessageManager
.getString("label.load_associated_tree"));
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ LoadtreeMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ scaleAbove.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleLeft.setVisible(false);
scaleLeft.setSelected(true);
scaleLeft.setText(MessageManager.getString("action.scale_left"));
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ scaleLeft.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleRight.setVisible(false);
scaleRight.setSelected(true);
scaleRight.setText(MessageManager.getString("action.scale_right"));
- scaleRight.addActionListener(new java.awt.event.ActionListener()
+ scaleRight.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
centreColumnLabelsMenuItem.setState(false);
centreColumnLabelsMenuItem.setText(MessageManager
.getString("label.centre_column_labels"));
- centreColumnLabelsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- centreColumnLabels_actionPerformed(e);
- }
- });
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
followHighlightMenuItem.setText(MessageManager
modifyPID.setText(MessageManager
.getString("label.modify_identity_thereshold"));
- modifyPID.addActionListener(new java.awt.event.ActionListener()
+ modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
modifyConservation.setText(MessageManager
.getString("label.modify_conservation_thereshold"));
- modifyConservation
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
sortByAnnotScore.setText(MessageManager
.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ sort.addMenuListener(new javax.swing.event.MenuListener()
{
@Override
showTranslation_actionPerformed(e);
}
});
+
+ /*
+ * cDNA menu options
+ */
+ cdna.setText(MessageManager.getString("label.cdna"));
+ // link to available cDNA
+ JMenuItem linkCdna = new JMenuItem(
+ MessageManager.getString("label.link_cdna"));
+ linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.link_cdna_tip")));
+ linkCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ linkCdna_actionPerformed();
+ }
+ });
+ cdna.add(linkCdna);
+ // align linked cDNA
+ JMenuItem alignCdna = new JMenuItem(
+ MessageManager.getString("label.align_cdna"));
+ alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.align_cdna_tip")));
+ alignCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ alignCdna_actionPerformed();
+ }
+ });
+ cdna.add(alignCdna);
+
+ // view alignment as cDNA (when known)
+ JMenuItem viewAsCdna = new JMenuItem(
+ MessageManager.getString("label.view_as_cdna"));
+ viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.view_as_cdna_tip")));
+ viewAsCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ viewAsCdna_actionPerformed();
+ }
+ });
+ cdna.add(viewAsCdna);
+
extractScores.setText(MessageManager.getString("label.extract_scores")
+ "...");
extractScores.addActionListener(new ActionListener()
extractScores_actionPerformed(e);
}
});
- extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
- // score extraction
+ 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"));
- /*
- * showProducts.addActionListener(new ActionListener() {
- *
- * public void actionPerformed(ActionEvent e) {
- * showProducts_actionPerformed(e); } });
- */
openFeatureSettings.setText(MessageManager
.getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
}
});
+ annotationColumn.setText(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
rnahelicesColour.setText(MessageManager
.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
hiddenMarkers_actionPerformed(e);
}
});
+
invertColSel.setText(MessageManager
.getString("action.invert_column_selection"));
- invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.ALT_MASK, false));
- invertColSel.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
invertColSel_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_focusGained(e);
}
});
+
save.setText(MessageManager.getString("action.save"));
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- save.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
+
newView.setText(MessageManager.getString("action.new_view"));
- newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- newView.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
idRightAlign_actionPerformed(e);
}
});
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
- gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, 0, false));
- gatherViews.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
gatherViews_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
- expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, 0, false));
- expandViews.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
expandViews_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
pageSetup
.setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
- viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(showAllAnnotations);
- viewMenu.add(hideAllAnnotations);
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllAlAnnotations);
+ annotationsMenu.add(hideAllAlAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllSeqAnnotations);
+ annotationsMenu.add(hideAllSeqAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
+ annotationsMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
// viewMenu.add(showSeqFeaturesHeight);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
+ calculateMenu.add(cdna);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
calculateMenu.add(sortByTree);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
+ jMenu2.add(createBioJS);
+ jMenu2.add(createSVG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
}
/**
+ * Adds the given action listener and key accelerator to the given menu item.
+ * Also saves in a lookup table to support lookup of action by key stroke.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
+ {
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
+ }
+
+ protected void viewAsCdna_actionPerformed()
+ {
+ }
+
+ protected void alignCdna_actionPerformed()
+ {
+ }
+
+ protected void linkCdna_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
* Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void showAllAnnotations_actionPerformed()
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
{
- setAllAnnotationsVisibility(true);
+ setAnnotationsVisibility(true, forSequences, forAlignment);
}
/**
* Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void hideAllAnnotations_actionPerformed()
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
{
- setAllAnnotationsVisibility(false);
+ setAnnotationsVisibility(false, forSequences, forAlignment);
}
/**
- * Set the visibility of all annotations to true or false.
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
*
* @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void setAllAnnotationsVisibility(boolean visible)
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
}
{
}
- protected void showProducts_actionPerformed(ActionEvent e)
- {
- }
-
protected void buildSortByAnnotationScoresMenu()
{
}
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
{
}
+ public void createSVG(java.io.File f)
+ {
+
+ }
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
+
+ protected boolean isShowAutoCalculatedAbove()
+ {
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
+ }
+
+ protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+ {
+ this.annotationSortOrder = annotationSortOrder;
+ }
+
+ public Map<KeyStroke, JMenuItem> getAccelerators()
+ {
+ return this.accelerators;
+ }
+
+ /**
+ * Returns the selected index of the tabbed pane, or -1 if none selected
+ * (including the case where the tabbed pane has not been made visible).
+ *
+ * @return
+ */
+ public int getTabIndex()
+ {
+ return tabbedPane.getSelectedIndex();
+ }
+
+ public JPanel getStatusPanel()
+ {
+ return statusPanel;
+ }
}
git://source.jalview.org / jalview.git / blobdiff