X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=e2f15e10ae7d54c2e3ca61e50995e9f4bbd6f088;hb=baa077bd19420018433d78927aad3ad139e47351;hp=c060ef00dbd88b23a6d4e86b6f924f83c9cfc25c;hpb=4dd40d33a5becefd51c31a426f2501b21029f82c;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c060ef0..e2f15e1 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -644,8 +644,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     conservation.description = "Conservation for group " + getName()
             + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
-            : endRes + 1)
+    int aWidth = (conservation.annotations != null)
+            ? (endRes < conservation.annotations.length
+                    ? conservation.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     conservation.annotations = null;
     conservation.annotations = new Annotation[aWidth]; // should be alignment
@@ -665,8 +667,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.description = "Percent Identity";
     consensusData = cnsns;
     // preserve width if already set
-    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
-            : endRes + 1)
+    int aWidth = (consensus.annotations != null)
+            ? (endRes < consensus.annotations.length
+                    ? consensus.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     consensus.annotations = null;
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
@@ -1334,11 +1338,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
-              .equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
-              && (label == null || (ann.label != null && ann.label
-                      .equals(label))))
+      if ((calcId == null || (ann.getCalcId() != null
+              && ann.getCalcId().equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null
+                      && ann.sequenceRef == seq))
+              && (label == null
+                      || (ann.label != null && ann.label.equals(label))))
       {
         aa.add(ann);
       }
@@ -1465,7 +1470,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public boolean isNucleotide()
   {
-    if (context != null) {
+    if (context != null)
+    {
       return context.isNucleotide();
     }
     return false;