Removed SuperGroup

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c90af98..a9a0e35 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -269,16 +269,6 @@ public class APopupMenu
 \r
   void refresh()\r
   {\r
-    SequenceGroup sg = getGroup();\r
-    if(sg!=null)\r
-    {\r
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
-      if (superG != null)\r
-      {\r
-        superG.setSuperGroupProperties(sg);\r
-      }\r
-        }\r
     ap.seqPanel.seqCanvas.repaint();\r
     if(ap.overviewPanel!=null)\r
       ap.overviewPanel.updateOverviewImage();\r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 78aa015..b4e2b3f 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -390,47 +390,7 @@ public class Alignment implements AlignmentI
         return ret;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param sg DOCUMENT ME!\r
-     */\r
-    public void addSuperGroup(SuperGroup sg)\r
-    {\r
-        superGroup.addElement(sg);\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param sg DOCUMENT ME!\r
-     */\r
-    public void removeSuperGroup(SuperGroup sg)\r
-    {\r
-        superGroup.removeElement(sg);\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param sg DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg)\r
-    {\r
-        for (int i = 0; i < this.superGroup.size(); i++)\r
-        {\r
-            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
 \r
-            if (temp.sequenceGroups.contains(sg))\r
-            {\r
-                return temp;\r
-            }\r
-        }\r
-\r
-        return null;\r
-    }\r
 \r
     /**    */\r
     public void addGroup(SequenceGroup sg)\r

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b93f178..6f22947 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -50,7 +50,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public float graphMax;\r
 \r
-    public java.util.Vector graphLines;\r
+    public GraphLine threshold;\r
 \r
     // Graphical hints and tips\r
 \r
@@ -233,21 +233,14 @@ public class AlignmentAnnotation
         return buffer.toString();\r
       }\r
 \r
-      public void addGraphLine(GraphLine line)\r
+      public void setThreshold(GraphLine line)\r
       {\r
-        if(graphLines==null)\r
-          graphLines = new java.util.Vector();\r
-\r
-        graphLines.addElement(line);\r
+        threshold = line;\r
       }\r
 \r
-      public GraphLine getGraphLine(int index)\r
+      public GraphLine getTrheshold()\r
       {\r
-        if(graphLines!=null && index<graphLines.size())\r
-          return (GraphLine)graphLines.elementAt(index);\r
-\r
-        else\r
-          return null;\r
+          return threshold;\r
       }\r
 \r
       public void adjustForAlignment()\r

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index ebd95d9..10ea154 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -219,28 +219,6 @@ public interface AlignmentI
      */\r
     public void deleteAllGroups();\r
 \r
-    /**\r
-     * Adds a super group. A SuperGroup is a group of groups.\r
-     *\r
-     * @param sg Adds a new SuperGroup to alignment\r
-     */\r
-    public void addSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Removes SuperGroup from alignment.\r
-     *\r
-     * @param sg This SuperGroup will be deleted from alignment.\r
-     */\r
-    public void removeSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Finds any SuperGroup that a given SequenceGroup may be part of.\r
-     *\r
-     * @param sg SequenceGroup to search for.\r
-     *\r
-     * @return SuperGroup that contains the given SequenceGroup.\r
-     */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg);\r
 \r
     /**\r
      * Adds a new AlignmentAnnotation to this alignment\r