inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index d26127a..14cb729 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -707,16 +707,19 @@ public final class AptxUtil {
                 nex.setIgnoreQuotes( false );
             }
         }
+        AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
         final Phylogeny[] phys = factory.create( url.openStream(), parser );
-        if ( nhx_or_nexus && internal_numbers_are_confidences ) {
-            for( final Phylogeny phy : phys ) {
-                PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+        if ( phys != null ) {
+            if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+                for( final Phylogeny phy : phys ) {
+                    PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+                }
             }
-        }
-        if ( midpoint_reroot ) {
-            for( final Phylogeny phy : phys ) {
-                PhylogenyMethods.midpointRoot( phy );
-                PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+            if ( midpoint_reroot ) {
+                for( final Phylogeny phy : phys ) {
+                    PhylogenyMethods.midpointRoot( phy );
+                    PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+                }
             }
         }
         return phys;