JAL-2349 reusable contact map holder for SequenceI and AnnotatedCollectionI

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 0aa8424..e1c87a9 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -26,7 +26,6 @@ import java.util.BitSet;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -2034,52 +2033,35 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
   }
 
-  Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
+  ////
+  //// Contact Matrix Holder Boilerplate
+  ////
+  ContactMapHolder cmholder = new ContactMapHolder();
 
   @Override
   public Collection<ContactMatrixI> getContactMaps()
   {
-    if (contactmaps != null && contactmaps.size() > 0)
-    {
-      return contactmaps.values();
-    }
-    return Collections.EMPTY_LIST;
+    return cmholder.getContactMaps();
   }
 
   @Override
   public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
-    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
-    if (cm == null)
-    {
-      return null;
-    }
-    return cm.getContactList(column);
+    return cmholder.getContactListFor(_aa, column);
   }
 
   @Override
   public AlignmentAnnotation addContactList(ContactMatrixI cm)
   {
+    AlignmentAnnotation aa = cmholder.addContactList(cm);
+
     Annotation _aa[] = new Annotation[getWidth()];
     Annotation dummy = new Annotation(0.0f);
     for (int i = 0; i < _aa.length; _aa[i++] = dummy)
     {
       ;
     }
-    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
-            "Contact Matrix", _aa);
-    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
-    aa.graphMin = cm.getMin();
-    aa.graphMax = cm.getMax();
-    aa.editable = false;
-    // aa.autoCalculated = true;
-    contactmaps.put(aa.annotationId, cm);
-    // TODO: contact matrices could be intra or inter - more than one refseq
-    // possible!
-    if (cm.hasReferenceSeq())
-    {
-      aa.setSequenceRef(cm.getReferenceSeq());
-    }
+    aa.annotations = _aa;
     addAnnotation(aa);
     return aa;
   }