Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[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 c0d1774..a6dd8b6 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
@@ -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);
@@ -416,7 +415,7 @@ public class Tree extends DatastoreItem
             }
             else
             {
-              System.err.println("WARNING: Unassociated treeNode "
+              jalview.bin.Console.errPrintln("WARNING: Unassociated treeNode "
                       + tnode.element().toString() + " "
                       + ((tnode.getName() != null)
                               ? " label " + tnode.getName()
@@ -467,7 +466,7 @@ 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;