X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=ab83ebfed2477a6649ed95ad9082077c01d3ea97;hb=fffc26ac5f8cf4eaa5faea6a7e369b94d381d859;hp=a457f2c3c978a78093eef300b35b6d7d1f4afc19;hpb=e2785e20355846acd9e81d50cf9a8a56b04ec095;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index a457f2c..ab83ebf 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -374,7 +374,7 @@ public final class SurfacingUtil {
                 }
                 for( int i = 0; i < nodes.size() - 1; ++i ) {
                     for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
+                        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ),
                                                                                             nodes.get( j ) );
                         String rank = "unknown";
                         if ( lca.getNodeData().isHasTaxonomy()
@@ -1192,16 +1192,30 @@ public final class SurfacingUtil {
                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
                     final List<Domain> domains = protein.getProteinDomains( domain_id );
                     if ( domains.size() > 0 ) {
-                        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-                        for( final Domain domain : domains ) {
-                            stats.addValue( domain.getPerSequenceEvalue() );
-                        }
                         out.write( protein.getSpecies().getSpeciesId() );
                         out.write( separator );
                         out.write( protein.getProteinId().getId() );
                         out.write( separator );
-                        out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
+                        out.write( domain_id.toString() );
+                        out.write( separator );
+                        for( final Domain domain : domains ) {
+                            out.write( "/" );
+                            out.write( domain.getFrom() + "-" + domain.getTo() );
+                        }
+                        out.write( "/" );
                         out.write( separator );
+                        out.write( "{" );
+                        boolean first = true;
+                        for( final Domain domain : protein.getProteinDomains() ) {
+                            if ( first ) {
+                                first = false;
+                            }
+                            else {
+                                out.write( "," );
+                            }
+                            out.write( domain.getDomainId().toString() );
+                        }
+                        out.write( "}" );
                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
                                 .equals( SurfacingConstants.NONE ) ) ) {
                             out.write( protein.getDescription() );