X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;fp=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=514a32662fdf2318a146249c0c9346daf7e01c0f;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=89ec5adeb95df1f6ab809560f205caf0c4fb5b2a;hpb=8288438dd58cfc2d1fe18a060afda0d647b85c32;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 89ec5ad..514a326 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2050,14 +2050,14 @@ public class Alignment implements AlignmentI, AutoCloseable
   public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
   {
     ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
-    if (cm==null && _aa.groupRef!=null)
+    if (cm == null && _aa.groupRef != null)
     {
       cm = _aa.groupRef.getContactMatrixFor(_aa);
     }
-    if (cm==null && _aa.sequenceRef!=null)
+    if (cm == null && _aa.sequenceRef != null)
     {
       cm = _aa.sequenceRef.getContactMatrixFor(_aa);
-      if (cm==null)
+      if (cm == null)
       {
         // TODO fix up this logic and unify with getContactListFor
         cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@@ -2087,7 +2087,7 @@ public class Alignment implements AlignmentI, AutoCloseable
                   && spos <= 1 + _aa.sequenceRef.getEnd())
           {
             cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
-                    spos-_aa.sequenceRef.getStart());
+                    spos - _aa.sequenceRef.getStart());
           }
         }
       }