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fixed some problems
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
analysis
/
AncestralTaxonomyInference.java
diff --git
a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index
e422508
..
da68994
100644
(file)
--- 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;
}
}
return;
}
- // if ( !n.getNodeData().isHasTaxonomy() ) {
- // n.getNodeData().setTaxonomy( new Taxonomy() );
- // }
final Taxonomy tax = new Taxonomy();
n.getNodeData().setTaxonomy( tax );
tax.setScientificName( last_common_lineage );
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 ) {
}
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;
phy.recalculateNumberOfExternalDescendants( true );
}
return not_found;