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(JAL-962) allow group visibility to be specified before features in those groups...
[jalview.git]
/
src
/
jalview
/
appletgui
/
FeatureRenderer.java
diff --git
a/src/jalview/appletgui/FeatureRenderer.java
b/src/jalview/appletgui/FeatureRenderer.java
index
39249cc
..
03f15d3
100755
(executable)
--- a/
src/jalview/appletgui/FeatureRenderer.java
+++ b/
src/jalview/appletgui/FeatureRenderer.java
@@
-1064,9
+1064,9
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
+ featureGroups.put(toset[i], new Boolean(visible));
if (st != null)
{
if (st != null)
{
- featureGroups.put(toset[i], new Boolean(visible));
rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
@@
-1090,6
+1090,7
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
}
}
}
}
+ ArrayList<String> hiddenGroups=new ArrayList<String>();
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
@@
-1103,8
+1104,10
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
{
featureGroups = new Hashtable();
}
{
featureGroups = new Hashtable();
}
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ hiddenGroups =new ArrayList<String>();
+ hiddenGroups.addAll(featureGroups.keySet());
+ ArrayList allFeatures = new ArrayList();
+ ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
for (int i = 0; i < av.alignment.getHeight(); i++)
SequenceFeature[] tmpfeatures;
String group;
for (int i = 0; i < av.alignment.getHeight(); i++)
@@
-1123,9
+1126,11
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
+ // Remove group from the hiddenGroup list
+ hiddenGroups.remove(group);
if (!allGroups.contains(group))
{
if (!allGroups.contains(group))
{
- allGroups.addElement(group);
+ allGroups.add(group);
boolean visible = true;
if (featureGroups.containsKey(group))
boolean visible = true;
if (featureGroups.containsKey(group))
@@
-1141,7
+1146,7
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
- allFeatures.addElement(tmpfeatures[index].getType());
+ allFeatures.add(tmpfeatures[index].getType());
}
index++;
}
}
index++;
}