X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=514a32662fdf2318a146249c0c9346daf7e01c0f;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=1ec702cf523b47413097c9d17e4bd2177f88a998;hpb=9e40070f757fc662aba39ba6314be4937276ead4;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1ec702c..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());
           }
         }
       }
@@ -2101,8 +2101,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     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)
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
     {
       ;
     }