*/
public void updateAnnotation()
{
- updateAnnotation(false);
+ updateAnnotation(false, false);
}
-
public void updateAnnotation(boolean applyGlobalSettings)
{
+ updateAnnotation(applyGlobalSettings,false);
+ }
+ public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings)
+ {
// TODO: this should be merged with other annotation update stuff - that
// sits on AlignViewport
boolean updateCalcs = false;
for (SequenceGroup sg:av.getAlignment().getGroups())
{
updateCalcs = false;
- if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.containsKey(sg)))
{
// set defaults for this group's conservation/consensus
sg.setshowSequenceLogo(showprf);