From 81bf67e64fade340738792bfbcd8b3a3efd3a010 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Feb 2006 15:20:26 +0000
Subject: [PATCH] Removed SuperGroup

---
 src/jalview/appletgui/APopupMenu.java          |   10 ------
 src/jalview/datamodel/Alignment.java           |   40 ------------------------
 src/jalview/datamodel/AlignmentAnnotation.java |   17 +++-------
 src/jalview/datamodel/AlignmentI.java          |   22 -------------
 4 files changed, 5 insertions(+), 84 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c90af98..a9a0e35 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -269,16 +269,6 @@ public class APopupMenu
 
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    if(sg!=null)
-    {
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-      if (superG != null)
-      {
-        superG.setSuperGroupProperties(sg);
-      }
-        }
     ap.seqPanel.seqCanvas.repaint();
     if(ap.overviewPanel!=null)
       ap.overviewPanel.updateOverviewImage();
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 78aa015..b4e2b3f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -390,47 +390,7 @@ public class Alignment implements AlignmentI
         return ret;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void addSuperGroup(SuperGroup sg)
-    {
-        superGroup.addElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void removeSuperGroup(SuperGroup sg)
-    {
-        superGroup.removeElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg)
-    {
-        for (int i = 0; i < this.superGroup.size(); i++)
-        {
-            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
 
-            if (temp.sequenceGroups.contains(sg))
-            {
-                return temp;
-            }
-        }
-
-        return null;
-    }
 
     /**    */
     public void addGroup(SequenceGroup sg)
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b93f178..6f22947 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -50,7 +50,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public float graphMax;
 
-    public java.util.Vector graphLines;
+    public GraphLine threshold;
 
     // Graphical hints and tips
 
@@ -233,21 +233,14 @@ public class AlignmentAnnotation
         return buffer.toString();
       }
 
-      public void addGraphLine(GraphLine line)
+      public void setThreshold(GraphLine line)
       {
-        if(graphLines==null)
-          graphLines = new java.util.Vector();
-
-        graphLines.addElement(line);
+        threshold = line;
       }
 
-      public GraphLine getGraphLine(int index)
+      public GraphLine getTrheshold()
       {
-        if(graphLines!=null && index<graphLines.size())
-          return (GraphLine)graphLines.elementAt(index);
-
-        else
-          return null;
+          return threshold;
       }
 
       public void adjustForAlignment()
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index ebd95d9..10ea154 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -219,28 +219,6 @@ public interface AlignmentI
      */
     public void deleteAllGroups();
 
-    /**
-     * Adds a super group. A SuperGroup is a group of groups.
-     *
-     * @param sg Adds a new SuperGroup to alignment
-     */
-    public void addSuperGroup(SuperGroup sg);
-
-    /**
-     * Removes SuperGroup from alignment.
-     *
-     * @param sg This SuperGroup will be deleted from alignment.
-     */
-    public void removeSuperGroup(SuperGroup sg);
-
-    /**
-     * Finds any SuperGroup that a given SequenceGroup may be part of.
-     *
-     * @param sg SequenceGroup to search for.
-     *
-     * @return SuperGroup that contains the given SequenceGroup.
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg);
 
     /**
      * Adds a new AlignmentAnnotation to this alignment
-- 
1.7.10.2