some fixes

[jalview.git] / forester / java / src / org / forester / phylogeny / data / Taxonomy.java

diff --git a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
index ee78912..d403a8e 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
+++ b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
@@ -230,7 +230,8 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
         return ( ( getIdentifier() == null ) && ForesterUtil.isEmpty( getTaxonomyCode() )
                 && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
                 && ForesterUtil.isEmpty( getRank() ) && ForesterUtil.isEmpty( _uris )
-                && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) && ForesterUtil.isEmpty( _lineage ) );
+                && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) && ForesterUtil
+                .isEmpty( _lineage ) );
     }
 
     /**
@@ -288,7 +289,7 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
     }
 
     public void setRank( final String rank ) {
-        if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS.contains( rank ) ) {
+        if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS_SET.contains( rank ) ) {
             throw new PhyloXmlDataFormatException( "illegal rank: [" + rank + "]" );
         }
         _rank = rank;
@@ -412,7 +413,7 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
         return 0;
     }
 
-    public void setLineage( List<String> lineage ) {
+    public void setLineage( final List<String> lineage ) {
         _lineage = lineage;
     }