in progress

[jalview.git] / forester / java / src / org / forester / io / parsers / phyloxml / PhyloXmlUtil.java

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
index 156c65a..e585cb3 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.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.io.parsers.phyloxml;
 
@@ -31,13 +31,15 @@ import java.util.List;
 import java.util.Set;
 import java.util.regex.Pattern;
 
+import org.forester.io.parsers.util.ParserUtils;
+
 public final class PhyloXmlUtil {
 
     public static final String       OTHER                                      = "other";
     public static final String       UNKNOWN                                    = "unknown";
     public final static Pattern      SEQUENCE_SYMBOL_PATTERN                    = Pattern.compile( "\\S{1,20}" );
     public final static Pattern      TAXOMONY_CODE_PATTERN                      = Pattern
-                                                                                        .compile( "[a-zA-Z0-9_]{1,10}" );
+                                                                                        .compile( ParserUtils.TAX_CODE );
     public final static Pattern      LIT_REF_DOI_PATTERN                        = Pattern
                                                                                         .compile( "[a-zA-Z0-9_\\.]+\\S+" );
     public final static Set<String>  SEQUENCE_TYPES                             = new HashSet<String>();
@@ -47,10 +49,13 @@ public final class PhyloXmlUtil {
     public static final String       VECTOR_PROPERTY_REF                        = "vector:index=";
     public static final String       VECTOR_PROPERTY_TYPE                       = "xsd:decimal";
     public static final String       UNIPROT_TAX_PROVIDER                       = "uniprot";
+    public static final String       SEQ_TYPE_RNA                               = "rna";
+    public static final String       SEQ_TYPE_DNA                               = "dna";
+    public static final String       SEQ_TYPE_PROTEIN                           = "protein";
     static {
-        SEQUENCE_TYPES.add( "rna" );
-        SEQUENCE_TYPES.add( "protein" );
-        SEQUENCE_TYPES.add( "dna" );
+        SEQUENCE_TYPES.add( SEQ_TYPE_RNA );
+        SEQUENCE_TYPES.add( SEQ_TYPE_PROTEIN );
+        SEQUENCE_TYPES.add( SEQ_TYPE_DNA );
         TAXONOMY_RANKS_LIST.add( "domain" );
         TAXONOMY_RANKS_LIST.add( "superkingdom" );
         TAXONOMY_RANKS_LIST.add( "kingdom" );