X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=5ea97fbe12f9bcd30763a300098f701d90046d26;hb=76fe44a302e9bd32938af7ee2b70b48d7f0d4c4b;hp=c0d17747201b0eb4ce215b05466dbcc4317aeee4;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index c0d1774..5ea97fb 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -358,7 +358,7 @@ public class Tree extends DatastoreItem
         }
         if (jvseq instanceof SequenceI)
         {
-          leaf.setElement(jvseq);
+          leaf.setElement((SequenceI) jvseq);
           leaf.setPlaceholder(false);
         }
         else
@@ -394,8 +394,7 @@ public class Tree extends DatastoreItem
       {
         if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
         {
-          Object assocseq = ((BinaryNode) tnode)
-                  .element();
+          Object assocseq = ((BinaryNode) tnode).element();
           if (assocseq instanceof SequenceI)
           {
             Vobject vobj = this.getjv2vObj(assocseq);
@@ -416,11 +415,12 @@ public class Tree extends DatastoreItem
             }
             else
             {
-              System.err.println("WARNING: Unassociated treeNode "
-                      + tnode.element().toString() + " "
-                      + ((tnode.getName() != null)
-                              ? " label " + tnode.getName()
-                              : ""));
+              jalview.bin.Console
+                      .errPrintln("WARNING: Unassociated treeNode "
+                              + tnode.element().toString() + " "
+                              + ((tnode.getName() != null)
+                                      ? " label " + tnode.getName()
+                                      : ""));
             }
           }
         }
@@ -467,7 +467,7 @@ public class Tree extends DatastoreItem
       occurence = Integer.valueOf(oval).intValue();
     } catch (Exception e)
     {
-      System.err.println("Invalid nodespec '" + nodespec + "'");
+      jalview.bin.Console.errPrintln("Invalid nodespec '" + nodespec + "'");
       return null;
     }
     jalview.datamodel.BinaryNode bn = null;