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JAL-3199 corrected sort menu items to JMenuItem
[jalview.git]
/
src
/
jalview
/
jbgui
/
GAlignFrame.java
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
e0db9ed
..
9491d33
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-28,6
+28,7
@@
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-77,7
+78,7
@@
public class GAlignFrame extends JInternalFrame
protected JMenu sortByAnnotScore = new JMenu();
protected JMenu sortByAnnotScore = new JMenu();
- public JLabel statusBar = new JLabel();
+ protected JLabel statusBar = new JLabel();
protected JMenu outputTextboxMenu = new JMenu();
protected JMenu outputTextboxMenu = new JMenu();
@@
-125,7
+126,7
@@
public class GAlignFrame extends JInternalFrame
protected JMenuItem modifyPID;
protected JMenuItem modifyPID;
- protected JMenuItem annotationColour;
+ protected JRadioButtonMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu sortByTreeMenu = new JMenu();
@@
-199,14
+200,16
@@
public class GAlignFrame extends JInternalFrame
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
- private SequenceAnnotationOrder annotationSortOrder;
-
- private boolean showAutoCalculatedAbove = false;
-
private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
+ protected JMenuItem sortAnnBySequence;
+
+ protected JMenuItem sortAnnByLabel;
+
+ protected JMenu annotationsMenu;
+
public GAlignFrame()
{
try
public GAlignFrame()
{
try
@@
-285,7
+288,7
@@
public class GAlignFrame extends JInternalFrame
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
- JMenu annotationsMenu = new JMenu(
+ annotationsMenu = new JMenu(
MessageManager.getString("action.annotations"));
JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
colourMenu.setText(MessageManager.getString("action.colour"));
MessageManager.getString("action.annotations"));
JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
colourMenu.setText(MessageManager.getString("action.colour"));
@@
-598,42
+601,27
@@
public class GAlignFrame extends JInternalFrame
hideAllAnnotations_actionPerformed(true, false);
}
});
hideAllAnnotations_actionPerformed(true, false);
}
});
- SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
- .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
+ sortAnnBySequence = new JMenuItem(
MessageManager.getString("label.sort_annotations_by_sequence"));
MessageManager.getString("label.sort_annotations_by_sequence"));
- final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
+ sortAnnByLabel = new JMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
MessageManager.getString("label.sort_annotations_by_label"));
- sortAnnBySequence.setSelected(
- sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
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();
+ setAnnotationSortOrder(SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnotations(false);
}
});
}
});
- sortAnnByLabel.setSelected(
- sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
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();
+ setAnnotationSortOrder(SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnotations(false);
}
});
colourTextMenuItem = new JCheckBoxMenuItem(
}
});
colourTextMenuItem = new JCheckBoxMenuItem(
@@
-884,14
+872,15
@@
public class GAlignFrame extends JInternalFrame
final boolean autoFirst = Cache
.getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
showAutoFirst.setSelected(autoFirst);
final boolean autoFirst = Cache
.getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
showAutoFirst.setSelected(autoFirst);
- setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showAutoFirst.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- setShowAutoCalculatedAbove(showAutoFirst.isSelected());
- sortAnnotations_actionPerformed();
+ if (setShowAutoCalculatedAbove(showAutoFirst.isSelected()))
+ {
+ sortAnnotations(true);
+ }
}
});
showAutoLast.setSelected(!showAutoFirst.isSelected());
}
});
showAutoLast.setSelected(!showAutoFirst.isSelected());
@@
-900,8
+889,10
@@
public class GAlignFrame extends JInternalFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- setShowAutoCalculatedAbove(!showAutoLast.isSelected());
- sortAnnotations_actionPerformed();
+ if (setShowAutoCalculatedAbove(!showAutoLast.isSelected()))
+ {
+ sortAnnotations(true);
+ }
}
});
}
});
@@
-1962,8
+1953,9
@@
public class GAlignFrame extends JInternalFrame
}
});
}
});
- annotationColour = new JMenuItem(
+ annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
annotationColour.addActionListener(new ActionListener()
{
@Override
annotationColour.addActionListener(new ActionListener()
{
@Override
@@
-2017,11
+2009,12
@@
public class GAlignFrame extends JInternalFrame
}
/**
}
/**
- * Action on clicking sort annotations by type.
+ * Action on clicking sort annotations by type, or change position of
+ * autocalculated annotation
*
*
- * @param sortOrder
+ * @param autoCalcOnly
*/
*/
- protected void sortAnnotations_actionPerformed()
+ protected void sortAnnotations(boolean autoCalcOnly)
{
}
{
}
@@
-2618,25
+2611,22
@@
public class GAlignFrame extends JInternalFrame
}
}
- protected boolean isShowAutoCalculatedAbove()
- {
- return showAutoCalculatedAbove;
- }
-
- protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
- {
- this.showAutoCalculatedAbove = showAutoCalculatedAbove;
- }
-
- protected SequenceAnnotationOrder getAnnotationSortOrder()
+ /**
+ * Sets the value of the flag for 'show autocalculated annotations above other
+ * annotations'. Answers true if the value changed, else false.
+ *
+ * @param showAutoCalculatedAbove
+ * @return
+ */
+ protected boolean setShowAutoCalculatedAbove(
+ boolean showAutoCalculatedAbove)
{
{
- return annotationSortOrder;
+ return false;
}
}
- protected void setAnnotationSortOrder(
+ public void setAnnotationSortOrder(
SequenceAnnotationOrder annotationSortOrder)
{
SequenceAnnotationOrder annotationSortOrder)
{
- this.annotationSortOrder = annotationSortOrder;
}
public Map<KeyStroke, JMenuItem> getAccelerators()
}
public Map<KeyStroke, JMenuItem> getAccelerators()