From 49d24119c8c55614fb78fba64333c02d3b4c52ae Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Sun, 24 Mar 2013 23:43:59 +0000 Subject: [PATCH] added transfer of taxonomy for GSDI --- forester/java/src/org/forester/sdi/GSDI.java | 6 +++--- forester/java/src/org/forester/sdi/GSDIR.java | 8 +------- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 44fb856..b9fa794 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -182,7 +182,7 @@ public final class GSDI implements GSDII { private static final void transferTaxonomy( final PhylogenyNode g, final PhylogenyNode s ) { if ( s.getNodeData().isHasTaxonomy() ) { - g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() ); + g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() ); if ( g.isInternal() ) { if ( g.getChildNode1().isInternal() ) { if ( g.getChildNode1().getNodeData().isHasTaxonomy() && g.getChildNode1().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) { @@ -201,12 +201,12 @@ public final class GSDI implements GSDII { if ( g.isInternal() ) { if ( g.getChildNode1().isInternal() ) { if ( g.getChildNode1().getName() == s.getName() ) { - g.getChildNode1().setName( "" ); + g.getChildNode1().setName( "" ); } } if ( g.getChildNode2().isInternal() ) { if ( g.getChildNode2().getName() == s.getName() ) { - g.getChildNode2().setName( "" ); + g.getChildNode2().setName( "" ); } } } diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java index 3615f31..6b170d9 100644 --- a/forester/java/src/org/forester/sdi/GSDIR.java +++ b/forester/java/src/org/forester/sdi/GSDIR.java @@ -80,13 +80,7 @@ public class GSDIR implements GSDII { for( final PhylogenyBranch branch : gene_tree_branches_post_order ) { reRoot( branch, gene_tree ); PhylogenyMethods.preOrderReId( species_tree ); - //TEST, remove later - // for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) { - // final PhylogenyNode g = it.next(); - // if ( g.isInternal() ) { - // g.setLink( null ); - // } - // } + final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree, true, min_duplications_sum ); -- 1.7.10.2