From 4548727494c3bf521eeec90a07e3bc6c0bdfb64e Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 10 Jun 2022 12:52:49 +0100
Subject: [PATCH] JAL-1551 formatting

---
 src/jalview/datamodel/Alignment.java |   29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 9825bff..ea04361 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,13 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.io.FastaFile;
-import jalview.util.Comparison;
-import jalview.util.LinkedIdentityHashSet;
-import jalview.util.MessageManager;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -41,6 +34,13 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
+import jalview.util.MessageManager;
+
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
@@ -1915,11 +1915,12 @@ public class Alignment implements AlignmentI, AutoCloseable
   @Override
   public boolean setHiddenColumns(HiddenColumns cols)
   {
-  boolean changed = cols == null ? hiddenCols != null
-          : !cols.equals(hiddenCols);
-  hiddenCols = cols;
-  return changed;
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
+    hiddenCols = cols;
+    return changed;
   }
+
   @Override
   public void setupJPredAlignment()
   {
@@ -2034,8 +2035,7 @@ public class Alignment implements AlignmentI, AutoCloseable
 
   Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
   @Override
-  public
-  ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
     ContactMatrixI cm = contactmaps.get(_aa.annotationId);
     if (cm == null)
@@ -2062,7 +2062,8 @@ public class Alignment implements AlignmentI, AutoCloseable
     aa.editable = false;
     // aa.autoCalculated = true;
     contactmaps.put(aa.annotationId, cm);
-    // TODO: contact matrices could be intra or inter - more than one refseq possible! 
+    // TODO: contact matrices could be intra or inter - more than one refseq
+    // possible!
     if (cm.hasReferenceSeq())
     {
       aa.setSequenceRef(cm.getReferenceSeq());
-- 
1.7.10.2