JAL-3210 Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8473904..b88ef3a 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -143,8 +143,8 @@ public class AlignmentSorter
     }
 
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    List<SequenceI> asq;
-    synchronized (asq = align.getSequences())
+    List<SequenceI> asq = align.getSequences();
+    synchronized (asq)
     {
       for (int i = 0; i < len; i++)
       {
@@ -179,10 +179,10 @@ public class AlignmentSorter
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    List<SequenceI> algn;
-    synchronized (algn = align.getSequences())
+    List<SequenceI> algn = align.getSequences();
+    synchronized (algn)
     {
-      List<SequenceI> tmp = new ArrayList<SequenceI>();
+      List<SequenceI> tmp = new ArrayList<>();
 
       for (int i = 0; i < seqs.length; i++)
       {
@@ -279,7 +279,7 @@ public class AlignmentSorter
   {
     // MAINTAINS ORIGNAL SEQUENCE ORDER,
     // ORDERS BY GROUP SIZE
-    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> groups = new ArrayList<>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -315,7 +315,7 @@ public class AlignmentSorter
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
 
     for (int i = 0; i < groups.size(); i++)
     {
@@ -357,7 +357,7 @@ public class AlignmentSorter
     // tmp2 = tmp.retainAll(mask);
     // return tmp2.addAll(mask.removeAll(tmp2))
 
-    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    ArrayList<SequenceI> seqs = new ArrayList<>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
@@ -436,7 +436,7 @@ public class AlignmentSorter
   {
     int nSeq = align.getHeight();
 
-    List<SequenceI> tmp = new ArrayList<SequenceI>();
+    List<SequenceI> tmp = new ArrayList<>();
 
     tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());