*/
package jalview.appletgui;
+import jalview.analysis.Conservation;
import jalview.datamodel.SequenceGroup;
import jalview.renderer.ResidueShaderI;
import jalview.util.MessageManager;
import java.awt.event.MouseListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
-import java.util.Iterator;
+import java.util.List;
public class SliderPanel extends Panel implements ActionListener,
AdjustmentListener, MouseListener
conservationSlider.setTitle(MessageManager.formatMessage(
"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())
{
sp.setAllGroupsCheckEnabled(true);
}
{
return;
}
-
- ResidueShaderI toChange = cs;
- Iterator<SequenceGroup> allGroups = null;
-
- if (allGroupsCheck.getState())
+ if (forConservation)
{
- allGroups = ap.av.getAlignment().getGroups().listIterator();
+ cs.setConservationApplied(true);
+ cs.setConservationInc(i);
+ }
+ else
+ {
+ cs.setThreshold(i, ap.av.isIgnoreGapsConsensus());
}
- while (toChange != null)
+ if (allGroupsCheck.getState())
{
- if (forConservation)
+ for (SequenceGroup group : ap.av.getAlignment().getGroups())
{
- toChange.setConservationInc(i);
- }
- else
- {
- toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
- }
- if (allGroups != null && allGroups.hasNext())
- {
- while ((toChange = allGroups.next().cs) == null
- && allGroups.hasNext())
+ ResidueShaderI groupColourScheme = group.getGroupColourScheme();
+ if (forConservation)
{
- ;
+ if (!groupColourScheme.conservationApplied())
+ {
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group",
+ group.getSequences(null), group.getStartRes(),
+ group.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ group.cs.setConservation(c);
+
+ }
+ groupColourScheme.setConservationApplied(true);
+ groupColourScheme.setConservationInc(i);
+ }
+ else
+ {
+ groupColourScheme.setThreshold(i, ap.av.isIgnoreGapsConsensus());
}
- }
- else
- {
- toChange = null;
}
}
ap.seqPanel.seqCanvas.repaint();
-
}
public void setAllGroupsCheckEnabled(boolean b)
{
+ allGroupsCheck.setState(ap.av.getColourAppliesToAllGroups());
allGroupsCheck.setEnabled(b);
}