From d6acbafc10c767f3bf58092258ca6ed0fd4c8dc2 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 10 Jun 2022 12:55:26 +0100
Subject: [PATCH] JAL-4027 getter for contact matrices on the Alignment.

---
 src/jalview/datamodel/Alignment.java  |   12 ++++++++++++
 src/jalview/datamodel/AlignmentI.java |    3 +++
 2 files changed, 15 insertions(+)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ea04361..0aa8424 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -2034,6 +2035,17 @@ public class Alignment implements AlignmentI, AutoCloseable
   }
 
   Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    if (contactmaps != null && contactmaps.size() > 0)
+    {
+      return contactmaps.values();
+    }
+    return Collections.EMPTY_LIST;
+  }
+
   @Override
   public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 862a2bf..93a8c26 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import java.util.Collection;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -635,4 +636,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
 
   AlignmentAnnotation addContactList(ContactMatrixI cm);
+
+  Collection<ContactMatrixI> getContactMaps();
 }
-- 
1.7.10.2