From: James Procter <j.procter@dundee.ac.uk>
Date: Sun, 14 May 2023 13:24:27 +0000 (+0100)
Subject: JAL-2349 fix up tests for Java 11 compatibility and require sequence associated mappa... 
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4080955a4825b990ebfb1df6208ee1728bea360c;p=jalview.git

JAL-2349 fix up tests for Java 11 compatibility and require sequence associated mappable matrix instance to have a mapping to the sequence it is associated with.
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5ae7195..2b331d7 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -39,6 +39,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
 
 /**
  * 
@@ -2151,6 +2152,10 @@ public class Sequence extends ASequence implements SequenceI
     }
     aa.annotations = _aa;
     aa.setSequenceRef(this);
+    if (cm instanceof MappableContactMatrix && !((MappableContactMatrix) cm).hasReferenceSeq())
+    {
+      ((MappableContactMatrix) cm).setRefSeq(this);
+    }
     aa.createSequenceMapping(this, getStart(), false);
     addAlignmentAnnotation(aa);
     return aa;
diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
index ae2b37c..9497d85 100644
--- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
@@ -55,7 +55,11 @@ public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
     return toSeq;
   }
 
-  protected void setRefSeq(SequenceI _refSeq)
+  /**
+   * set the reference sequence and construct the mapping between the start-end positions of given sequence and row/columns of contact matrix
+   * @param _refSeq
+   */
+  public void setRefSeq(SequenceI _refSeq)
   {
     refSeq = _refSeq;
     while (refSeq.getDatasetSequence() != null)
diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index d496097..d48d539 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -382,7 +382,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
         }
       }
     }
-    return ContactMatrixI.super.getGroupsFor(column);
+    return super.getGroupsFor(column);
   }
 
   HashMap<BitSet,Color> colorMap = new HashMap<>();
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 4baa384..54093ee 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2626,6 +2626,11 @@ public class AlignmentUtilsTests
                     && al.getAlignmentAnnotation().length == 1);
     AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
             .iterator().next();
+    ContactMatrixI t_cm = al.getContactMatrixFor(alan);
+    assertNotNull("No contact map for the transferred annotation row.",t_cm);
+    assertTrue(t_cm instanceof SeqDistanceContactMatrix);
+    assertTrue(((SeqDistanceContactMatrix)t_cm).hasReferenceSeq());
+    
     ContactListI cl = al.getContactListFor(alan, 1);
     assertNotNull(
             "No contact matrix recovered after reference annotation transfer",