JAL-653 hold AlignedCodonFrame collections as list rather than set

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 26b7d48..b497824 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -43,10 +43,8 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.Vector;
 
 import MCview.Atom;
@@ -70,7 +68,7 @@ public class StructureSelectionManager
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
 
   private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
 
@@ -929,13 +927,13 @@ public class StructureSelectionManager
   /**
    * Add each of the given codonFrames to the stored set, if not aready present.
    * 
-   * @param set
+   * @param mappings
    */
-  public void registerMappings(Set<AlignedCodonFrame> set)
+  public void registerMappings(List<AlignedCodonFrame> mappings)
   {
-    if (set != null)
+    if (mappings != null)
     {
-      for (AlignedCodonFrame acf : set)
+      for (AlignedCodonFrame acf : mappings)
       {
         registerMapping(acf);
       }
@@ -1147,4 +1145,9 @@ public class StructureSelectionManager
     }
     return null;
   }
+
+  public List<AlignedCodonFrame> getSequenceMappings()
+  {
+    return seqmappings;
+  }
 }