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JAL-4153 avoid use of invokeAndWait, increase wait time and add timeout for the cache...
[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)
{
}
if (jvseq instanceof SequenceI)
{
- leaf.setElement(jvseq);
+ leaf.setElement((SequenceI) jvseq);
leaf.setPlaceholder(false);
}
else
leaf.setPlaceholder(false);
}
else
@@
-394,8
+394,7
@@
public class Tree extends DatastoreItem
{
if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
{
{
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);
if (assocseq instanceof SequenceI)
{
Vobject vobj = this.getjv2vObj(assocseq);
@@
-416,7
+415,7
@@
public class Tree extends DatastoreItem
}
else
{
}
else
{
- System.err.println("WARNING: Unassociated treeNode "
+ jalview.bin.Console.errPrintln("WARNING: Unassociated treeNode "
+ tnode.element().toString() + " "
+ ((tnode.getName() != null)
? " label " + tnode.getName()
+ 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)
{
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;
return null;
}
jalview.datamodel.BinaryNode bn = null;