}
}
}
-
+ // <<<<<<< HEAD
+ //
+ // =======
+ // if (minmax == null)
+ // {
+ // minmax = new Hashtable<String, float[][]>();
+ // }
+ //
+ // Set<String> oldGroups = new HashSet<String>(featureGroups.keySet());
+ // >>>>>>> refs/heads/develop
AlignmentI alignment = av.getAlignment();
List<String> allfeatures = new ArrayList<String>(); // or HashSet?
SequenceI asq = alignment.getSequenceAt(i);
for (String group : asq.getFeatures().getFeatureGroups(true))
{
- if (group == null)
- {
- continue;
- }
- Boolean groupDisplayed = featureGroups.get(group);
- if (groupDisplayed == null)
+ // <<<<<<< HEAD
+ /*
+ * features in null group are always displayed; other groups
+ * keep their current visibility; new groups as 'newMadeVisible'
+ */
+ boolean groupDisplayed = true;
+ if (group != null)
+ // =======
+ // continue;
+ // }
+ //
+ // int index = 0;
+ // while (index < features.length)
+ // {
+ // String fgrp = features[index].getFeatureGroup();
+ // oldGroups.remove(fgrp);
+ // if (!featuresDisplayed.isRegistered(features[index].getType()))
+ // >>>>>>> refs/heads/develop
{
- groupDisplayed = Boolean.valueOf(newMadeVisible);
- featureGroups.put(group, groupDisplayed);
+ // <<<<<<< HEAD
+ if (featureGroups.containsKey(group))
+ // =======
+ // if (fgrp != null)
+ // >>>>>>> refs/heads/develop
+ {
+ groupDisplayed = featureGroups.get(group);
+ }
+ else
+ {
+ groupDisplayed = newMadeVisible;
+ featureGroups.put(group, groupDisplayed);
+ }
}
if (groupDisplayed)
{
}
/*
+ //<<<<<<< HEAD
* mark any new feature types as visible
*/
Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
setOrder(type, 0);
}
}
+ // =======
+ // * oldGroups now consists of groups that no longer
+ // * have any feature in them - remove these
+ // */
+ // for (String grp : oldGroups)
+ // {
+ // featureGroups.remove(grp);
+ // >>>>>>> refs/heads/develop
}
updateRenderOrder(allfeatures);
public List<String> getDisplayedFeatureGroups()
{
List<String> _gps = new ArrayList<String>();
- boolean valid = false;
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
{
- valid = true;
_gps.add(gp);
}
- if (!valid)
- {
- return null;
- }
- else
- {
- // gps = new String[_gps.size()];
- // _gps.toArray(gps);
- }
}
return _gps;
}