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applet gsdi
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
sdi
/
GSDIR.java
diff --git
a/forester/java/src/org/forester/sdi/GSDIR.java
b/forester/java/src/org/forester/sdi/GSDIR.java
index
8ada705
..
80a0d3a
100644
(file)
--- a/
forester/java/src/org/forester/sdi/GSDIR.java
+++ b/
forester/java/src/org/forester/sdi/GSDIR.java
@@
-77,13
+77,18
@@
public class GSDIR implements GSDII {
gene_tree.reRoot( branch );
\r
PhylogenyMethods.preOrderReId( species_tree );
\r
//TEST, remove later
\r
gene_tree.reRoot( branch );
\r
PhylogenyMethods.preOrderReId( species_tree );
\r
//TEST, remove later
\r
- // for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {
\r
+ // for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
\r
// final PhylogenyNode g = it.next();
\r
// if ( g.isInternal() ) {
\r
// g.setLink( null );
\r
// }
\r
// }
\r
// final PhylogenyNode g = it.next();
\r
// if ( g.isInternal() ) {
\r
// g.setLink( null );
\r
// }
\r
// }
\r
- final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree, true );
\r
+ final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
\r
+ true,
\r
+ min_duplications_sum );
\r
+ if ( gsdi_result == null ) {
\r
+ continue;
\r
+ }
\r
if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
\r
min_duplications_sum = gsdi_result.getDuplicationsSum();
\r
speciations_sum = gsdi_result.getSpeciationsSum();
\r
if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
\r
min_duplications_sum = gsdi_result.getDuplicationsSum();
\r
speciations_sum = gsdi_result.getSpeciationsSum();
\r