in progress

[jalview.git] / forester / java / src / org / forester / ws / seqdb / UniProtTaxonomy.java

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
index 145569d..2cdd93e 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.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.ws.seqdb;
 
@@ -32,48 +32,19 @@ import org.forester.util.ForesterUtil;
 
 public final class UniProtTaxonomy {
 
-    private static final String         ARCHAEA                  = "Archaea";
-    private static final String         BACTERIA                 = "Bacteria";
-    private static final String         EUKARYOTA                = "Eukaryota";
-    private final List<String>          _lineage;
-    private final String                _code;
-    private final String                _scientific_name;
-    private final String                _common_name;
-    private final String                _synonym;
-    private final String                _rank;
-    private final String                _id;
-    public final static String          CELLULAR_ORGANISMS       = "cellular organisms";
-    public final static String          VIRUSES                  = "Viruses";
-    public final static UniProtTaxonomy DROSOPHILA_GENUS         = new UniProtTaxonomy( new String[] {
-            CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
-            "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" },
-                                                                                        "",
-                                                                                        "fruit flies",
-                                                                                        "Drosophila",
-                                                                                        "",
-                                                                                        "genus",
-                                                                                        "7215" );
-    public final static UniProtTaxonomy XENOPUS_GENUS            = new UniProtTaxonomy( new String[] {
-            CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Amphibia",
-            "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae", "Xenopus" },
-                                                                                        "",
-                                                                                        "",
-                                                                                        "Xenopus",
-                                                                                        "",
-                                                                                        "genus",
-                                                                                        "8353" );
-    public final static UniProtTaxonomy CAPITELLA_TELATA_SPECIES = new UniProtTaxonomy( new String[] {
-            CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Annelida", "Polychaeta", "Scolecida", "Capitellida",
-            "Capitellidae", "Capitella", "Capitella teleta"                            },
-                                                                                        "",
-                                                                                        "",
-                                                                                        "Capitella teleta",
-                                                                                        "Capitella sp. I",
-                                                                                        "species",
-                                                                                        "283909" );
-
-    // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] {
-    //         CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" );
+    private static final String ARCHAEA            = "Archaea";
+    private static final String BACTERIA           = "Bacteria";
+    private static final String EUKARYOTA          = "Eukaryota";
+    private final List<String>  _lineage;
+    private final String        _code;
+    private final String        _scientific_name;
+    private final String        _common_name;
+    private final String        _synonym;
+    private final String        _rank;
+    private final String        _id;
+    public final static String  CELLULAR_ORGANISMS = "cellular organisms";
+    public final static String  VIRUSES            = "Viruses";
+
     public UniProtTaxonomy( final String line ) {
         final String[] items = line.split( "\t" );
         if ( items.length < 5 ) {