JAL-4290 Set structureSelectionManager settings more generically and when no desktop...

[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 1ac7bab..5ea97fb 100644 (file)
--- 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
@@ -415,11 +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()
+                                      : ""));
             }
           }
         }
@@ -466,7 +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;