X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=259030f74c496f6131b171482e37c98521606f5c;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=244b650a13306cf81f8fe34282fdd638f9bce1e7;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 244b650..259030f 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -786,10 +786,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     av.featuresDisplayed = new Hashtable();
     Vector allfeatures = new Vector();
     minmax = new Hashtable();
-
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment=av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+      SequenceFeature[] features = alignment.getSequenceAt(i)
               .getSequenceFeatures();
 
       if (features == null)
@@ -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]);
+        featureGroups.put(toset[i], new Boolean(visible));
         if (st != null)
         {
-          featureGroups.put(toset[i], new Boolean(visible));
           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)
@@ -1103,29 +1104,34 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       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++)
+    AlignmentI alignment=av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
       {
         continue;
       }
 
       alignmentHasFeatures = true;
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {
         if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
+          // Remove group from the hiddenGroup list
+          hiddenGroups.remove(group);
           if (!allGroups.contains(group))
           {
-            allGroups.addElement(group);
+            allGroups.add(group);
 
             boolean visible = true;
             if (featureGroups.containsKey(group))
@@ -1141,7 +1147,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
         if (!allFeatures.contains(tmpfeatures[index].getType()))
         {
-          allFeatures.addElement(tmpfeatures[index].getType());
+          allFeatures.add(tmpfeatures[index].getType());
         }
         index++;
       }
@@ -1170,16 +1176,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     Vector allFeatures = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment=av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
       {
         continue;
       }
 
       alignmentHasFeatures = true;
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {