*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.datamodel.SequenceGroup;
import jalview.jbgui.GSliderPanel;
import jalview.renderer.ResidueShaderI;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
+import java.util.List;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
"label.conservation_colour_increment",
new String[] { source == null ? BACKGROUND : source }));
- if (ap.av.getAlignment().getGroups() != null)
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ if (groups != null && !groups.isEmpty())
{
sliderPanel.setAllGroupsCheckEnabled(true);
}
{
ap.av.setThreshold(percent);
}
- updateColourScheme(percent, cs);
+ updateColourScheme(percent, cs, null);
if (allGroupsCheck.isSelected())
{
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ for (SequenceGroup sg : groups)
{
- updateColourScheme(percent, sg.getGroupColourScheme());
+ updateColourScheme(percent, sg.getGroupColourScheme(), sg);
}
}
*
* @param percent
* @param scheme
+ * @param sg
*/
- protected void updateColourScheme(int percent, ResidueShaderI scheme)
+ protected void updateColourScheme(int percent, ResidueShaderI scheme,
+ SequenceGroup sg)
{
if (scheme == null)
{
}
if (forConservation)
{
+ if (!scheme.conservationApplied())
+ {
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
+
+ }
+ scheme.setConservationApplied(true);
scheme.setConservationInc(percent);
}
else
public void setAllGroupsCheckEnabled(boolean b)
{
allGroupsCheck.setEnabled(b);
+ allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
}
/**