inprogress

[jalview.git] / forester / java / src / org / forester / io / parsers / nhx / NHXParser.java

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 8846374..d40e3f8 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -46,7 +46,6 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
@@ -596,13 +595,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                         }
                         node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
                     }
-                    else if ( s.startsWith( NHXtags.DOMAIN_STRUCTURE ) ) {
-                        if ( !node_to_annotate.getNodeData().isHasSequence() ) {
-                            node_to_annotate.getNodeData().setSequence( new Sequence() );
-                        }
-                        node_to_annotate.getNodeData().getSequence()
-                                .setDomainArchitecture( new DomainArchitecture( s.substring( 3 ) ) );
-                    }
                     else if ( s.startsWith( NHXtags.SEQUENCE_ACCESSION ) ) {
                         if ( !node_to_annotate.getNodeData().isHasSequence() ) {
                             node_to_annotate.getNodeData().setSequence( new Sequence() );
@@ -711,6 +703,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     }
 
     public static enum TAXONOMY_EXTRACTION {
-        NO, AGRESSIVE, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT;
+        NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT, AGGRESSIVE;
     }
 }