From 69ef8ad030b982bf5c7403be8e860ab5645683fa Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Wed, 20 Jun 2012 05:23:53 +0000 Subject: [PATCH] gsdi work --- forester/java/src/org/forester/sdi/GSDI.java | 58 ++++++++++++++------------ 1 file changed, 31 insertions(+), 27 deletions(-) diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 5fd72bb..8e2cdf0 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -339,39 +339,43 @@ public final class GSDI extends SDI { continue; } else { - throw new IllegalArgumentException( "gene tree node [" + g + "] has no taxonomic data" ); + throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" ); } } - final String tax_str = taxonomyToString( g, tax_comp_base ); - if ( ForesterUtil.isEmpty( tax_str ) ) { - if ( _strip_gene_tree ) { - _stripped_gene_tree_nodes.add( g ); - continue; - } - else { - throw new IllegalArgumentException( "gene tree node [" + g + "] has no appropriate taxonomic data" ); - } - } - final PhylogenyNode s = speciestree_ext_nodes.get( tax_str ); - if ( s == null ) { - if ( _strip_gene_tree ) { - _stripped_gene_tree_nodes.add( g ); + else { + final String tax_str = taxonomyToString( g, tax_comp_base ); + if ( ForesterUtil.isEmpty( tax_str ) ) { + if ( _strip_gene_tree ) { + _stripped_gene_tree_nodes.add( g ); + } + else { + throw new IllegalArgumentException( "gene tree node " + g + + " has no appropriate taxonomic data" ); + } } else { - throw new IllegalArgumentException( "taxonomy [" + g.getNodeData().getTaxonomy() - + "] not present in species tree" ); + final PhylogenyNode s = speciestree_ext_nodes.get( tax_str ); + // if ( s == null ) { + // if ( _strip_gene_tree ) { + // _stripped_gene_tree_nodes.add( g ); + // } + // else { + // throw new IllegalArgumentException( "taxonomy " + g.getNodeData().getTaxonomy() + // + " not present in species tree" ); + // } + // } + // else { + g.setLink( s ); + System.out.println( "setting link of " + g + " to " + s ); + // } } } - else { - g.setLink( s ); - System.out.println( "setting link of " + g + " to " + s ); - } - if ( _strip_gene_tree ) { - for( final PhylogenyNode n : _stripped_gene_tree_nodes ) { - if ( _gene_tree.getNode( n.getId() ) != null ) { - _gene_tree.deleteSubtree( _gene_tree.getNode( n.getId() ), true ); - } - } + } // for loop + if ( _strip_gene_tree ) { + for( final PhylogenyNode n : _stripped_gene_tree_nodes ) { + // if ( _gene_tree.getNode( n.getId() ) != null ) { + _gene_tree.deleteSubtree( n, true ); + // } } } } -- 1.7.10.2