*/
package jalview.jbgui;
-import jalview.analysis.AnnotationSorter.SortOrder;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.schemes.ColourSchemeProperty;
JMenuItem showAllhidden = new JMenuItem();
- protected JMenuItem showAllAnnotations = new JMenuItem();
+ protected JMenuItem showAllSeqAnnotations = new JMenuItem();
- protected JMenuItem hideAllAnnotations = new JMenuItem();
+ protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAlAnnotations = new JMenuItem();
protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem sortAnnByType = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showAutoFirst = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showAutoLast = new JCheckBoxMenuItem();
+
private JMenuItem grpsFromSelection = new JMenuItem();
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
public GAlignFrame()
{
try
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);
}
});
sortAnnBySequence.setText(MessageManager
@Override
public void actionPerformed(ActionEvent e)
{
- sortAnnBySequence.setEnabled(false);
- sortAnnBySequence.setState(true);
- sortAnnByType.setEnabled(true);
- sortAnnByType.setState(false);
- sortAnnotations_actionPerformed(SortOrder.SEQUENCE_AND_TYPE);
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
- sortAnnByType.setText(MessageManager
- .getString("label.sort_annotations_by_type"));
- sortAnnByType.addActionListener(new ActionListener()
+ sortAnnByLabel.setText(MessageManager
+ .getString("label.sort_annotations_by_label"));
+ sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- sortAnnByType.setEnabled(false);
- sortAnnByType.setState(true);
- sortAnnBySequence.setEnabled(true);
+ boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setState(false);
- sortAnnotations_actionPerformed(SortOrder.TYPE_AND_SEQUENCE);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
colourTextMenuItem.setText(MessageManager
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
}
+ });
+ showAutoFirst.setText(MessageManager.getString("label.show_first"));
+ showAutoFirst.setState(Cache.getDefault("SHOW_AUTOCALC_ABOVE", false));
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean sortFirst = showAutoFirst.getState();
+ setShowAutoCalculatedAbove(sortFirst);
+ showAutoLast.setState(!sortFirst);
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setText(MessageManager.getString("label.show_last"));
+ showAutoLast.setState(!showAutoFirst.getState());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean sortLast = showAutoLast.getState();
+ setShowAutoCalculatedAbove(!sortLast);
+ showAutoFirst.setState(!sortLast);
+ sortAnnotations_actionPerformed();
+ }
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
annotationsMenu.add(annotationPanelMenuItem);
- annotationsMenu.add(showAllAnnotations);
- annotationsMenu.add(hideAllAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllAlAnnotations);
+ annotationsMenu.add(hideAllAlAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllSeqAnnotations);
+ annotationsMenu.add(hideAllSeqAnnotations);
annotationsMenu.add(sortAnnBySequence);
- annotationsMenu.add(sortAnnByType);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
*
* @param sortOrder
*/
- protected void sortAnnotations_actionPerformed(SortOrder 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)
{
}
// 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff