added AGRESSIVE tax extraction ^^

[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 4f6d146..b354921 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
+++ b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.phylogeny.data;
 
@@ -34,13 +34,10 @@ import org.forester.io.parsers.nhx.NHXtags;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
-import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 
 public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonomy> {
 
-    
-    
     private String       _scientific_name;
     private String       _common_name;
     private List<String> _synonyms;
@@ -329,17 +326,9 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
     }
 
     public void setTaxonomyCode( final String taxonomy_code ) throws PhyloXmlDataFormatException {
-        if ( ForesterConstants.TAXONOMY_CODE_STRICT ) {
-            if ( !ForesterUtil.isEmpty( taxonomy_code )
-                    && !PhyloXmlUtil.TAXOMONY_CODE_PATTERN_STRICT.matcher( taxonomy_code ).matches() ) {
-                throw new PhyloXmlDataFormatException( "illegal taxonomy code: [" + taxonomy_code + "]" );
-            }
-        }
-        else {
-            if ( !ForesterUtil.isEmpty( taxonomy_code )
-                    && !PhyloXmlUtil.TAXOMONY_CODE_PATTERN_LAX.matcher( taxonomy_code ).matches() ) {
-                throw new PhyloXmlDataFormatException( "illegal taxonomy code: [" + taxonomy_code + "]" );
-            }
+        if ( !ForesterUtil.isEmpty( taxonomy_code )
+                && !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( taxonomy_code ).matches() ) {
+            throw new PhyloXmlDataFormatException( "illegal taxonomy code: [" + taxonomy_code + "]" );
         }
         _taxonomy_code = taxonomy_code;
     }