Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 9d2f601..b0bb372 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -23,7 +23,7 @@ package jalview.appletgui;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -56,13 +56,12 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.Vector;
 
 public class FeatureSettings extends Panel implements ItemListener,
         MouseListener, MouseMotionListener, ActionListener,
@@ -370,36 +369,36 @@ public class FeatureSettings extends Panel implements ItemListener,
   // Group selection states
   void resetTable(boolean groupsChanged)
   {
-    SequenceFeature[] tmpfeatures;
-    String group = null, type;
-    Vector<String> visibleChecks = new Vector<String>();
+    List<String> displayableTypes = new ArrayList<String>();
     Set<String> foundGroups = new HashSet<String>();
+
     AlignmentI alignment = av.getAlignment();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
-      {
-        continue;
-      }
+      SequenceI seq = alignment.getSequenceAt(i);
 
-      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
-      int index = 0;
-      while (index < tmpfeatures.length)
+      /*
+       * get the sequence's groups for positional features
+       * and keep track of which groups are visible
+       */
+      Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+      Set<String> visibleGroups = new HashSet<String>();
+      for (String group : groups)
       {
-        group = tmpfeatures[index].featureGroup;
-        foundGroups.add(group);
-
-        if (group == null || checkGroupState(group))
+        if (group == null || fr.checkGroupVisibility(group, true))
         {
-          type = tmpfeatures[index].getType();
-          if (!visibleChecks.contains(type))
-          {
-            visibleChecks.addElement(type);
-          }
+          visibleGroups.add(group);
         }
-        index++;
       }
+
+      /*
+       * get distinct feature types for visible groups
+       * record distinct visible types
+       */
+      Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+              visibleGroups.toArray(new String[visibleGroups.size()]));
+      displayableTypes.addAll(types);
     }
 
     /*
@@ -416,7 +415,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     {
       comps = featurePanel.getComponents();
       check = (MyCheckbox) comps[i];
-      if (!visibleChecks.contains(check.type))
+      if (!displayableTypes.contains(check.type))
       {
         featurePanel.remove(i);
         cSize--;
@@ -433,24 +432,24 @@ public class FeatureSettings extends Panel implements ItemListener,
       {
         String item = rol.get(ro);
 
-        if (!visibleChecks.contains(item))
+        if (!displayableTypes.contains(item))
         {
           continue;
         }
 
-        visibleChecks.removeElement(item);
+        displayableTypes.remove(item);
 
         addCheck(false, item);
       }
     }
 
-    // now add checkboxes which should be visible,
-    // if they have not already been added
-    Enumeration<String> en = visibleChecks.elements();
-
-    while (en.hasMoreElements())
+    /*
+     * now add checkboxes which should be visible,
+     * if they have not already been added
+     */
+    for (String type : displayableTypes)
     {
-      addCheck(groupsChanged, en.nextElement().toString());
+      addCheck(groupsChanged, type);
     }
 
     featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),