From 830579e2492ae116119ff92c60157a570a0f5674 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 17 Sep 2011 18:03:59 +0000 Subject: [PATCH] fixed some problems --- .../src/org/forester/analysis/AncestralTaxonomyInference.java | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java index e422508..da68994 100644 --- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java +++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java @@ -242,9 +242,6 @@ public final class AncestralTaxonomyInference { } return; } - // if ( !n.getNodeData().isHasTaxonomy() ) { - // n.getNodeData().setTaxonomy( new Taxonomy() ); - // } final Taxonomy tax = new Taxonomy(); n.getNodeData().setTaxonomy( tax ); tax.setScientificName( last_common_lineage ); @@ -329,8 +326,10 @@ public final class AncestralTaxonomyInference { } if ( delete ) { for( final PhylogenyNode node : not_found_external_nodes ) { - phy.deleteSubtree( node, false ); + phy.deleteSubtree( node, true ); } + phy.externalNodesHaveChanged(); + phy.hashIDs(); phy.recalculateNumberOfExternalDescendants( true ); } return not_found; -- 1.7.10.2