JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[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..e4e0b6c 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)
       {
@@ -517,7 +517,7 @@ public class Tree extends DatastoreItem
    * referenced in input data has already been associated with jalview objects.
    * 
    * @param tp
-   * @param alignFrame
+   * @param loaderFrame
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */