X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FTaxonomyUtil.java;h=a8f38990a987b1acebf21daca1524d57378beb77;hb=5ea47511ea9c077b4b4709bed68ac31d6eee0477;hp=38c8da249ad0a5f514df9e8cd1c4ae9bdb9c03f9;hpb=17dce416188e13160d9bf0840bb370e3adca041e;p=jalview.git

diff --git a/forester/java/src/org/forester/util/TaxonomyUtil.java b/forester/java/src/org/forester/util/TaxonomyUtil.java
index 38c8da2..a8f3899 100644
--- a/forester/java/src/org/forester/util/TaxonomyUtil.java
+++ b/forester/java/src/org/forester/util/TaxonomyUtil.java
@@ -9,16 +9,15 @@ public final class TaxonomyUtil {
     public static String getTaxGroupByTaxCode( final String code ) {
         return _default_taxcode_taxgroup_map.get( code );
     }
-    
+
     public static int getTaxIdFromFakeTaxCode( final String code ) {
-       return FAKE_CODE_TO_ID_MAP.get( code );
+        return FAKE_CODE_TO_ID_MAP.get( code );
     }
-    
+
     public static boolean isHasTaxIdFromFakeTaxCode( final String code ) {
         return FAKE_CODE_TO_ID_MAP.containsKey( code );
-     }
-    
-    private final static Map<String, String> _default_taxcode_taxgroup_map = new HashMap<String, String>();
+    }
+    private final static Map<String, String>  _default_taxcode_taxgroup_map = new HashMap<String, String>();
     static {
         _default_taxcode_taxgroup_map.put( "HUMAN", "deuterostomia" );
         _default_taxcode_taxgroup_map.put( "HOMSA", "deuterostomia" );
@@ -91,6 +90,11 @@ public final class TaxonomyUtil {
         _default_taxcode_taxgroup_map.put( "BRAFL", "deuterostomia" );
         _default_taxcode_taxgroup_map.put( "SACKO", "deuterostomia" );
         _default_taxcode_taxgroup_map.put( "STRPU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "FICAL", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "OPHHA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PYTBI", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "LYTVA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PATMI", "deuterostomia" );
         _default_taxcode_taxgroup_map.put( "DROSE", "protostomia" );
         _default_taxcode_taxgroup_map.put( "DROSI", "protostomia" );
         _default_taxcode_taxgroup_map.put( "DROME", "protostomia" );
@@ -289,6 +293,7 @@ public final class TaxonomyUtil {
         _default_taxcode_taxgroup_map.put( "PICAB", "embryophyta" );
         _default_taxcode_taxgroup_map.put( "SELML", "embryophyta" );
         _default_taxcode_taxgroup_map.put( "PHYPA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "AMBTC", "embryophyta" );
         _default_taxcode_taxgroup_map.put( "OSTLU", "chlorophyta" );
         _default_taxcode_taxgroup_map.put( "ORCXX", "chlorophyta" );
         _default_taxcode_taxgroup_map.put( "OSTTA", "chlorophyta" );
@@ -323,6 +328,8 @@ public final class TaxonomyUtil {
         _default_taxcode_taxgroup_map.put( "TETTS", "alveolata" );
         _default_taxcode_taxgroup_map.put( "OTRXX", "alveolata" );
         _default_taxcode_taxgroup_map.put( "BLEJA", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "PERM5", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "ICHMG", "alveolata" );
         _default_taxcode_taxgroup_map.put( "FCYXX", "stramenopiles" );
         _default_taxcode_taxgroup_map.put( "PHATR", "stramenopiles" );
         _default_taxcode_taxgroup_map.put( "THAPS", "stramenopiles" );
@@ -543,37 +550,34 @@ public final class TaxonomyUtil {
         _default_taxcode_taxgroup_map.put( "HELPH", "bacteria" );
         _default_taxcode_taxgroup_map.put( "AQUAE", "bacteria" );
     }
-    
-    private final static Map<String,Integer> FAKE_CODE_TO_ID_MAP = new  HashMap<String,Integer>();
-
+    private final static Map<String, Integer> FAKE_CODE_TO_ID_MAP           = new HashMap<String, Integer>();
     static {
-        FAKE_CODE_TO_ID_MAP.put( "CTEXX", 283909);
-        FAKE_CODE_TO_ID_MAP.put( "HMAXX", 6085);
-        FAKE_CODE_TO_ID_MAP.put( "SARXX", 72019);
-        FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408);
-        FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344);
-        FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275);
-        FAKE_CODE_TO_ID_MAP.put( "BCOXX", 430998);
-        FAKE_CODE_TO_ID_MAP.put( "APPXX", 178873);
-        FAKE_CODE_TO_ID_MAP.put( "APMXX", 46634);
-        FAKE_CODE_TO_ID_MAP.put( "APSXX", 1042127);
-        FAKE_CODE_TO_ID_MAP.put( "CPUXX", 80637);
-        FAKE_CODE_TO_ID_MAP.put( "JARXX", 202697);
-        FAKE_CODE_TO_ID_MAP.put( "FPIXX", 40483);
-        FAKE_CODE_TO_ID_MAP.put( "PPLXX", 104341);
-        FAKE_CODE_TO_ID_MAP.put( "MVNXX", 1069443);
-        FAKE_CODE_TO_ID_MAP.put( "CREXX", 61392);
-        FAKE_CODE_TO_ID_MAP.put( "FALXX", 691883);
-        FAKE_CODE_TO_ID_MAP.put( "CCLXX", 85681);
-        FAKE_CODE_TO_ID_MAP.put( "ORCXX", 385169);
-        FAKE_CODE_TO_ID_MAP.put( "ASCXX", 763042);
-        FAKE_CODE_TO_ID_MAP.put( "CSUXX", 574566);
-        FAKE_CODE_TO_ID_MAP.put( "OTRXX", 1172189);
-        FAKE_CODE_TO_ID_MAP.put( "FCYXX", 186039);
-        FAKE_CODE_TO_ID_MAP.put( "AKEXX", 702273);
-        FAKE_CODE_TO_ID_MAP.put( "SAGXX", 876976);
-        FAKE_CODE_TO_ID_MAP.put( "ALIXX", 87102);
-        FAKE_CODE_TO_ID_MAP.put( "TTRXX", 529818);
-
+        FAKE_CODE_TO_ID_MAP.put( "CTEXX", 283909 );
+        FAKE_CODE_TO_ID_MAP.put( "HMAXX", 6085 );
+        FAKE_CODE_TO_ID_MAP.put( "SARXX", 72019 );
+        FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408 );
+        FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344 );
+        FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275 );
+        FAKE_CODE_TO_ID_MAP.put( "BCOXX", 430998 );
+        FAKE_CODE_TO_ID_MAP.put( "APPXX", 178873 );
+        FAKE_CODE_TO_ID_MAP.put( "APMXX", 46634 );
+        FAKE_CODE_TO_ID_MAP.put( "APSXX", 1042127 );
+        FAKE_CODE_TO_ID_MAP.put( "CPUXX", 80637 );
+        FAKE_CODE_TO_ID_MAP.put( "JARXX", 202697 );
+        FAKE_CODE_TO_ID_MAP.put( "FPIXX", 40483 );
+        FAKE_CODE_TO_ID_MAP.put( "PPLXX", 104341 );
+        FAKE_CODE_TO_ID_MAP.put( "MVNXX", 1069443 );
+        FAKE_CODE_TO_ID_MAP.put( "CREXX", 61392 );
+        FAKE_CODE_TO_ID_MAP.put( "FALXX", 691883 );
+        FAKE_CODE_TO_ID_MAP.put( "CCLXX", 85681 );
+        FAKE_CODE_TO_ID_MAP.put( "ORCXX", 385169 );
+        FAKE_CODE_TO_ID_MAP.put( "ASCXX", 763042 );
+        FAKE_CODE_TO_ID_MAP.put( "CSUXX", 574566 );
+        FAKE_CODE_TO_ID_MAP.put( "OTRXX", 1172189 );
+        FAKE_CODE_TO_ID_MAP.put( "FCYXX", 186039 );
+        FAKE_CODE_TO_ID_MAP.put( "AKEXX", 702273 );
+        FAKE_CODE_TO_ID_MAP.put( "SAGXX", 876976 );
+        FAKE_CODE_TO_ID_MAP.put( "ALIXX", 87102 );
+        FAKE_CODE_TO_ID_MAP.put( "TTRXX", 529818 );
     }
 }