JAL-3705 unit test and "fix" borrowing unused schema attribute

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index aa130cc..00e4fbc 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -271,14 +271,14 @@ public class Tree extends DatastoreItem
    * @return vector of alignment sequences in order of SeqCigar array (but
    *         missing unfound seqcigars)
    */
-  private Vector findAlignmentSequences(AlignmentI jal,
+  private Vector<SequenceI> findAlignmentSequences(AlignmentI jal,
           SeqCigar[] sequences)
   {
     SeqCigar[] tseqs = new SeqCigar[sequences.length];
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
-    Vector alsq = new Vector();
-    List<SequenceI> jalsqs;
-    synchronized (jalsqs = jal.getSequences())
+    Vector<SequenceI> alsq = new Vector<>();
+    List<SequenceI> jalsqs = jal.getSequences();
+    synchronized (jalsqs)
     {
       for (SequenceI asq : jalsqs)
       {
@@ -443,7 +443,7 @@ public class Tree extends DatastoreItem
     Integer nindx = (Integer) nodespecs.get(nname);
     if (nindx == null)
     {
-      nindx = new Integer(1);
+      nindx = Integer.valueOf(1);
     }
     nname = nindx.toString() + " " + nname;
     return nname;
@@ -465,7 +465,7 @@ public class Tree extends DatastoreItem
     String oval = nodespec.substring(0, nodespec.indexOf(' '));
     try
     {
-      occurence = new Integer(oval).intValue();
+      occurence = Integer.valueOf(oval).intValue();
     } catch (Exception e)
     {
       System.err.println("Invalid nodespec '" + nodespec + "'");