From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 18 May 2023 16:12:01 +0000 (+0100)
Subject: JAL-4134 column grouping model and methods moved to their own object held by by Conta... 
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~24
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc3341f9d1465b0226d184be4216d022a62e5cee;p=jalview.git

JAL-4134 column grouping model and methods moved to their own object held by by ContactMatrixI implementors
---

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index b72e3c7..fedbae3 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -318,7 +318,7 @@
 			<xs:element name="groups" type="xs:string" minOccurs="0"
 				maxOccurs="unbounded">
 				<xs:annotation>
-					<xs:documentation>Comma separated series of BigIntegers formed from
+					<xs:documentation>Comma separated series of longs formed from
 						bitsets defining partitions on the rows/columns of the matrix
 					</xs:documentation>
 				</xs:annotation>
diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 65fd01c..8f0afdf 100644
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -160,53 +160,18 @@ public abstract class ContactMatrix implements ContactMatrixI
   {
     return "Contact Matrix";
   }
-  List<BitSet> groups=null;
+  GroupSet grps = new GroupSet();
   @Override
-  public void updateGroups(List<BitSet> colGroups)
+  public GroupSetI getGroupSet()
   {
-    groups = colGroups;
-    colorMap=new HashMap<>();
+    return grps;
   }
   @Override
-  public boolean hasGroups()
+  public void setGroupSet(GroupSet makeGroups)
   {
-    return groups!=null && groups.size()>0;
-  }
-  @Override
-  public List<BitSet> getGroups()
-  {
-    return groups;
-  }
-  @Override
-  public BitSet getGroupsFor(int column)
-  {
-    for (BitSet gp:groups) {
-      if (gp.get(column))
-      {
-        return gp;
-      }
-    }
-    return ContactMatrixI.super.getGroupsFor(column);
-  }
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
-  {
-    if (bs==null) {
-      return Color.white;
-    }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
-    {
-      return Color.white;
-    }
-    return groupCol;
-  }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
-  {
-    colorMap.put(bs,color);
+    grps = makeGroups;
   }
+
   public static String contactToFloatString(ContactMatrixI cm)
   {
     StringBuilder sb = new StringBuilder();
diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index ba2ee48..256d43d 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -27,21 +27,41 @@ public interface ContactMatrixI
   int getWidth();
   int getHeight();
   
+  public GroupSetI getGroupSet();
+  
+  /// proxy methods to simplify use of the interface
+  /// Mappable contact matrices can override these to perform mapping
+  
+  default public boolean hasGroupSet()
+  {
+    return getGroupSet()!=null;
+  }
+
   default boolean hasGroups() {
-    return false;
+    return hasGroupSet() && getGroupSet().hasGroups();
   }
+
+
   default BitSet getGroupsFor(int column) {
+    if (!hasGroupSet())
+    {
     BitSet colbitset  = new BitSet();
     colbitset.set(column);
     return colbitset;
+    }
+    return getGroupSet().getGroupsFor(column);
   }
 
   default List<BitSet> getGroups() {
+    if (!hasGroupSet())
+    {
     return Arrays.asList();
+    } 
+    return getGroupSet().getGroups();
   }
 
   default boolean hasTree() {
-    return false;
+    return hasGroupSet() ? getGroupSet().hasTree() : false;
   }
 
   /**
@@ -49,25 +69,49 @@ public interface ContactMatrixI
    * @return null unless hasTree is true
    */
   default String getNewick() {
-    return null;
+    return hasGroupSet() ? getGroupSet().getNewick(): null;
   }
 
   default String getTreeMethod() {
-    return null;
+    return hasGroupSet() ? getGroupSet().getTreeMethod() :null;
   }
 
   default boolean hasCutHeight() {
-    return false;
+    return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
   }
 
   default double getCutHeight() {
-    return 0;
+    return hasGroupSet() ? getGroupSet().getCutHeight():0;
   }
 
-  void updateGroups(List<BitSet> colGroups);
+  default void updateGroups(List<BitSet> colGroups)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().updateGroups(colGroups);
+    }
+  }
 
-  void setColorForGroup(BitSet bs, Color color);
+  default void setColorForGroup(BitSet bs, Color color)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().setColorForGroup(bs, color);
+    }
+  }
+
+  default Color getColourForGroup(BitSet bs)
+  {
+    if (hasGroupSet())
+    {
+      return getGroupSet().getColourForGroup(bs);
+    }
+    else
+    {
+      return Color.white;
+    }
+  }
 
-  default Color getColourForGroup(BitSet bs) { return Color.white;}
+  void setGroupSet(GroupSet makeGroups);
 
 }
diff --git a/src/jalview/datamodel/GroupSet.java b/src/jalview/datamodel/GroupSet.java
new file mode 100644
index 0000000..b4d3e64
--- /dev/null
+++ b/src/jalview/datamodel/GroupSet.java
@@ -0,0 +1,191 @@
+package jalview.datamodel;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+
+public class GroupSet implements GroupSetI
+{
+  List<BitSet> groups = Arrays.asList();
+
+  public GroupSet(GroupSet grps)
+  {
+    abs=grps.abs;
+    colorMap=new HashMap<BitSet, Color>(grps.colorMap);
+    groups=new ArrayList<BitSet>(grps.groups);
+    newick=grps.newick;
+    thresh=grps.thresh;
+    treeType=grps.treeType;
+  }
+
+  public GroupSet()
+  {
+    // TODO Auto-generated constructor stub
+  }
+
+  public GroupSet(boolean abs2, float thresh2, List<BitSet> groups2,
+          String treeType2, String newick2)
+  {
+    abs = abs2;
+    thresh = thresh2;
+    groups = groups2;
+    treeType = treeType2;
+    newick=newick2;
+  }
+
+  @Override
+  public boolean hasGroups()
+  {
+    return groups != null;
+  }
+
+  String newick = null;
+
+  @Override
+  public String getNewick()
+  {
+    return newick;
+  }
+
+  @Override
+  public boolean hasTree()
+  {
+    return newick != null && newick.length() > 0;
+  }
+
+  boolean abs=false;
+
+  double thresh=0;
+
+  String treeType = null;
+
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    if (colGroups != null)
+    {
+      groups = colGroups;
+    }
+  }
+
+  @Override
+  public BitSet getGroupsFor(int column)
+  {
+    if (groups != null)
+    {
+      for (BitSet gp : groups)
+      {
+        if (gp.get(column))
+        {
+          return gp;
+        }
+      }
+    }
+    // return singleton set;
+    BitSet bs = new BitSet();
+    bs.set(column);
+    return bs;
+  }
+
+  HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+  @Override
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs == null)
+    {
+      return Color.white;
+    }
+    Color groupCol = colorMap.get(bs);
+    if (groupCol == null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+
+  @Override
+  public void setColorForGroup(BitSet bs, Color color)
+  {
+    colorMap.put(bs, color);
+  }
+
+  @Override
+  public void restoreGroups(List<BitSet> newgroups, String treeMethod,
+          String tree, double thresh2)
+  {
+    treeType = treeMethod;
+    groups = newgroups;
+    thresh = thresh2;
+    newick = tree;
+
+  }
+
+  @Override
+  public boolean hasCutHeight()
+  {
+    return groups != null && thresh != 0;
+  }
+
+  @Override
+  public double getCutHeight()
+  {
+    return thresh;
+  }
+
+  @Override
+  public String getTreeMethod()
+  {
+    return treeType;
+  }
+
+  public static GroupSet makeGroups(ContactMatrixI matrix, float thresh,
+          boolean abs)
+  {
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+            matrix);
+    double height = clusterer.findHeight(clusterer.getTopNode());
+    String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
+            true).print();
+    String treeType = "UPGMA";
+    Console.trace("Newick string\n" + newick);
+
+    List<BinaryNode> nodegroups;
+    if (abs ? height > thresh : 0 < thresh && thresh < 1)
+    {
+      float cut = abs ? (float) (thresh / height) : thresh;
+      Console.debug("Threshold " + cut + " for height=" + height);
+
+      nodegroups = clusterer.groupNodes(cut);
+    }
+    else
+    {
+      nodegroups = new ArrayList<BinaryNode>();
+      nodegroups.add(clusterer.getTopNode());
+    }
+    List<BitSet> groups = new ArrayList<>();
+    for (BinaryNode root : nodegroups)
+    {
+      BitSet gpset = new BitSet();
+      for (BinaryNode leaf : clusterer.findLeaves(root))
+      {
+        gpset.set((Integer) leaf.element());
+      }
+      groups.add(gpset);
+    }
+    GroupSet grps = new GroupSet(abs,thresh,groups,treeType, newick);
+    return grps;
+  }
+
+  @Override
+  public List<BitSet> getGroups()
+  {
+    return groups;
+  }
+}
diff --git a/src/jalview/datamodel/GroupSetI.java b/src/jalview/datamodel/GroupSetI.java
new file mode 100644
index 0000000..7c086a5
--- /dev/null
+++ b/src/jalview/datamodel/GroupSetI.java
@@ -0,0 +1,34 @@
+package jalview.datamodel;
+
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
+public interface GroupSetI
+{
+  boolean hasGroups();
+
+  String getNewick();
+
+  boolean hasTree();
+
+  void updateGroups(List<BitSet> colGroups);
+
+  BitSet getGroupsFor(int column);
+
+  Color getColourForGroup(BitSet bs);
+
+  void setColorForGroup(BitSet bs, Color color);
+
+  void restoreGroups(List<BitSet> newgroups, String treeMethod, String tree,
+          double thresh2);
+
+  boolean hasCutHeight();
+
+  double getCutHeight();
+
+  String getTreeMethod();
+
+  List<BitSet> getGroups();
+
+}
diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index f6377b1..ec19b25 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -111,42 +111,6 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
   {
     return width;
   }
-  private List<BitSet> groups=null;
-  @Override
-  public void updateGroups(List<BitSet> colGroups)
-  {
-    groups = colGroups;
-  }
-  @Override
-  public boolean hasGroups()
-  {
-    return groups!=null;
-  }
-  @Override
-  public List<BitSet> getGroups()
-  {
-    return groups;
-  }  
-
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
-  {
-    if (bs==null) {
-      return Color.white;
-    }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
-    {
-      return Color.white;
-    }
-    return groupCol;
-  }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
-  {
-    colorMap.put(bs,color);
-  }
   @Override
   protected double getElementAt(int _column, int i)
   {
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 52a6066..d781ebb 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -428,7 +428,7 @@ public class AnnotationLabels extends JPanel
       {
         final PAEContactMatrix cm = (PAEContactMatrix) av
                 .getContactMatrix(aa[selectedRow]);
-        if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0)
+        if (cm!=null && cm.hasTree())
         {
           item = new JMenuItem("Show Tree for Matrix");
           item.addActionListener(new ActionListener()
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 333c62b..a2ded9f 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -96,6 +96,7 @@ import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Point;
 import jalview.datamodel.RnaViewerModel;
@@ -2323,8 +2324,7 @@ public class Jalview2XML
               {
                 for (BitSet gp: cm.getGroups())
                 {
-                  BigInteger val = new BigInteger(gp.toByteArray());
-                  xmlmat.getGroups().add(val.toString());
+                  xmlmat.getGroups().add(stringifyBitset(gp));
                 }
               }
               if (cm.hasTree())
@@ -2478,6 +2478,38 @@ public class Jalview2XML
 
   }
 
+  private String stringifyBitset(BitSet gp) {
+    StringBuilder sb = new StringBuilder();
+    for (long val:gp.toLongArray())
+    {
+      if (sb.length()>0) {
+        sb.append(",");
+      }
+      sb.append(val);
+    }
+    return sb.toString();
+  }
+  private BitSet deStringifyBitset(String stringified) {
+    if ("".equals(stringified) || stringified==null)
+    {
+      return new BitSet();
+    }
+    String[] longvals = stringified.split(",");
+    long[] newlongvals = new long[longvals.length];
+    for (int lv=0;lv<longvals.length;lv++)
+    {
+      try {
+      newlongvals[lv]=Long.valueOf(longvals[lv]);
+      } catch (Exception x)
+      {
+        errorMessage+="Couldn't destringify bitset from: '"+stringified+"'";
+        newlongvals[lv]=0;
+      }
+    }
+    return BitSet.valueOf(newlongvals);
+
+    
+  }
   private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
   {
     AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
@@ -4030,20 +4062,12 @@ public class Jalview2XML
 
                     mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(),m.getMapToUnit().intValue());
                   }
-                  PAEContactMatrix newpae = new PAEContactMatrix(
-                          jaa.sequenceRef, mapping, elements);
                   List<BitSet> newgroups=new ArrayList<BitSet>();
                   if (xmlmat.getGroups().size()>0)
                   {
                     for (String sgroup:xmlmat.getGroups())
                     {
-                      try {
-                        BigInteger group = new BigInteger(sgroup);
-                        newgroups.add(BitSet.valueOf(group.toByteArray()));
-                      } catch (NumberFormatException nfe)
-                      {
-                        Console.error("Problem parsing groups for a contact matrix (\""+sgroup+"\"",nfe);
-                      }
+                      newgroups.add(deStringifyBitset(sgroup));
                     }
                   }
                   String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null;
@@ -4055,7 +4079,10 @@ public class Jalview2XML
                   
                   String treeMethod = xmlmat.getTreeMethod();
                   double thresh = xmlmat.getCutHeight()!=null ? xmlmat.getCutHeight() : 0;
-                  newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
+                  GroupSet grpset = new GroupSet();
+                  grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
+                  PAEContactMatrix newpae = new PAEContactMatrix(
+                          jaa.sequenceRef, mapping, elements,grpset);
                   jaa.sequenceRef.addContactListFor(jaa, newpae);
                 }
               }
diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
index 55a136a..27665d4 100644
--- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
@@ -5,6 +5,8 @@ import java.util.ArrayList;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.util.MapList;
@@ -32,6 +34,21 @@ public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
   {
     return refSeq;
   }
+  /**
+   * container for groups - defined on matrix columns
+   */
+  GroupSet grps=new GroupSet();
+  @Override
+  public GroupSetI getGroupSet()
+  {
+    return grps;
+  };
+  @Override
+  public void setGroupSet(GroupSet makeGroups)
+  {
+    grps = makeGroups;
+  }
+
   @Override
   public MapList getMapFor(SequenceI mapSeq)
   {
diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index d48d539..0ba9584 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -23,6 +23,8 @@ import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
 import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceI;
@@ -94,12 +96,14 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
    * @param newRefSeq
    * @param newFromMapList
    * @param elements2
+   * @param grps2 
    */
   public PAEContactMatrix(SequenceI newRefSeq,
-          MapList newFromMapList, float[][] elements2)
+          MapList newFromMapList, float[][] elements2, GroupSet grps2)
   {
     this(newRefSeq,elements2);
     toSeq = newFromMapList;
+    grps= grps2;
   }
 
   /**
@@ -307,127 +311,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     return length;
   }
-  List<BitSet> groups=null;
-  @Override
-  public boolean hasGroups()
-  {
-    return groups!=null;
-  }
-  String newick=null;
-  @Override
-  public String getNewick()
-  {
-    return newick;
-  }
-  @Override
-  public boolean hasTree()
-  {
-    return newick!=null && newick.length()>0;
-  }
-  boolean abs;
-  double thresh;
-  String treeType=null;
-  public void makeGroups(float thresh,boolean abs)
-  {
-    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
-    double height = clusterer.findHeight(clusterer.getTopNode());
-    newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
-    treeType = "UPGMA";
-    Console.trace("Newick string\n"+newick);
-
-    List<BinaryNode> nodegroups;
-    if (abs ? height > thresh : 0 < thresh && thresh < 1)
-    {
-      float cut = abs ? (float) (thresh / height) : thresh;
-      Console.debug("Threshold "+cut+" for height="+height);
-
-      nodegroups = clusterer.groupNodes(cut);
-    }
-    else
-    {
-      nodegroups = new ArrayList<BinaryNode>();
-      nodegroups.add(clusterer.getTopNode());
-    }
-    this.abs=abs;
-    this.thresh=thresh;
-    groups = new ArrayList<>();
-    for (BinaryNode root:nodegroups)
-    {
-      BitSet gpset=new BitSet();
-      for (BinaryNode leaf:clusterer.findLeaves(root))
-      {
-        gpset.set((Integer)leaf.element());
-      }
-      groups.add(gpset);
-    }
-  }
-  @Override
-  public void updateGroups(List<BitSet> colGroups)
-  {
-    if (colGroups!=null)
-    {
-      groups=colGroups;
-    }    
-  }
-  @Override
-  public BitSet getGroupsFor(int column)
-  {
-    if (groups != null)
-    {
-      for (BitSet gp : groups)
-      {
-        if (gp.get(column))
-        {
-          return gp;
-        }
-      }
-    }
-    return super.getGroupsFor(column);
-  }
-
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
-  {
-    if (bs==null) {
-      return Color.white;
-    }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
-    {
-      return Color.white;
-    }
-    return groupCol;
-  }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
-  {
-    colorMap.put(bs,color);
-  }
-  public void restoreGroups(List<BitSet> newgroups, String treeMethod,
-          String tree, double thresh2)
-  {
-    treeType=treeMethod;
-    groups = newgroups;
-    thresh=thresh2;
-    newick =tree;
-    
-  }
-  @Override
-  public boolean hasCutHeight() {
-    return groups!=null && thresh!=0;
-  }
-  @Override
-  public double getCutHeight()
-  {
-    return thresh;
-  }
-  @Override
-  public String getTreeMethod()
-  {
-    return treeType;
-  }
-
+  
   public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
   {
     FileInputStream infile=null;
@@ -458,7 +342,8 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   protected PAEContactMatrix newMappableContactMatrix(
           SequenceI newRefSeq, MapList newFromMapList)
   {
-      return new PAEContactMatrix(newRefSeq, newFromMapList,
-              elements);
+    PAEContactMatrix pae=new PAEContactMatrix(newRefSeq, newFromMapList,
+              elements, new GroupSet(grps));
+    return pae;
   } 
 }
diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index d9cbbd9..5d88e89 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -44,6 +44,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -442,7 +443,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) paeDict);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
+    matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     pdbAlignment.addAnnotation(cmannot);
@@ -496,7 +497,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
             (Map<String, Object>) pae_obj);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
+    matrix.setGroupSet(GroupSet.makeGroups(matrix,5f, true));
     AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     sm.getSequence().addAlignmentAnnotation(cmannot);
 
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 343df05..d038c78 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -32,7 +32,9 @@ import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
+import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
@@ -59,6 +61,7 @@ import jalview.datamodel.ContactMatrix;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
@@ -1568,10 +1571,36 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
     float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
     assertEquals(vals[3][4],paevals[3][4]);
-    dummyMat.makeGroups(0.5f, false);
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat,0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
+    // verify store/restore of group bitsets
+    for (BitSet  gp:dummyMat.getGroups())
+    {
+      StringBuilder sb = new StringBuilder();
+      for (long val:gp.toLongArray())
+      {
+        if (sb.length()>0) {
+          sb.append(",");
+        }
+        sb.append(val);
+      }
+      String[] longvals = sb.toString().split(",");
+      long[] newlongvals = new long[longvals.length];
+      for (int lv=0;lv<longvals.length;lv++)
+      {
+        try {
+        newlongvals[lv]=Long.valueOf(longvals[lv]);
+        } catch (Exception x)
+        {
+          Assert.fail("failed to deserialise bitset element ");
+        }
+      }
+      BitSet newGp = BitSet.valueOf(newlongvals);
+      assertTrue(gp.equals(newGp));
+    }
+    
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
             ".jvp");
     new Jalview2XML(false).saveState(tfile);