JAL-3210 Barebones gradle/buildship/eclipse. See README

[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 e4e0b6c..00e4fbc 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -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 + "'");
@@ -517,7 +517,7 @@ public class Tree extends DatastoreItem
    * referenced in input data has already been associated with jalview objects.
    * 
    * @param tp
-   * @param loaderFrame
+   * @param alignFrame
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */