X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FTaxonomyUtil.java;h=ef3856339a9006a0f12243ab293c189383421f55;hb=806db7d96607fa04c73ecfcfd8d46fbf41c3e85d;hp=496c9391fc289bfe55336201538a6f091e77cfb7;hpb=657f1b11d016bc2614075cfdd80b27701da408f0;p=jalview.git

diff --git a/forester/java/src/org/forester/util/TaxonomyUtil.java b/forester/java/src/org/forester/util/TaxonomyUtil.java
index 496c939..ef38563 100644
--- a/forester/java/src/org/forester/util/TaxonomyUtil.java
+++ b/forester/java/src/org/forester/util/TaxonomyUtil.java
@@ -26,6 +26,9 @@ public final class TaxonomyUtil {
     }
     private final static Map<String, String>  _default_taxcode_taxgroup_map = new HashMap<String, String>();
     static {
+        put( "BUFBU", "deuterostomia" );
+        put( "NOTVI", "deuterostomia" );
+        put( "SIRIN", "deuterostomia" );
         put( "ASTMX", "deuterostomia" );
         put( "CALMI", "deuterostomia" );
         put( "FICAL", "deuterostomia" );
@@ -166,6 +169,12 @@ public final class TaxonomyUtil {
         put( "SCHMA", "protostomia" );
         put( "CLOSI", "protostomia" );
         put( "SCHMD", "protostomia" );
+        put( "ANOGL", "protostomia" );
+        put( "BLAGE", "protostomia" );
+        put( "ZOONE", "protostomia" );
+        put( "SCHAM", "protostomia" );
+        put( "GRYPE", "protostomia" );
+        put( "ONCFA", "protostomia" );
         put( "ACRDI", "cnidaria" );
         put( "NEMVE", "cnidaria" );
         put( "HYDVU", "cnidaria" );
@@ -173,7 +182,8 @@ public final class TaxonomyUtil {
         put( "MNELE", "ctenophora" );
         put( "AMPQE", "porifera" );
         put( "MONBE", "choanoflagellida" );
-        put( "SALS5", "choanoflagellida" );
+        put( "SALS5", "choanoflagellida" ); //TODO remove me
+        put( "SALR5", "choanoflagellida" );
         put( "AMOPA", "ichthyophonida & filasterea" );
         put( "SARXX", "ichthyophonida & filasterea" );
         put( "CAPO3", "ichthyophonida & filasterea" );
@@ -361,6 +371,7 @@ public final class TaxonomyUtil {
         put( "ALIXX", "stramenopiles" );
         put( "BLAHO", "stramenopiles" );
         put( "BIGNA", "rhizaria" );
+        put( "RETFI", "rhizaria" );
         put( "TRYB2", "excavata" );
         put( "TRYCR", "excavata" );
         put( "LEIMA", "excavata" );
@@ -568,6 +579,7 @@ public final class TaxonomyUtil {
         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( "SPHAR", 72019 ); //TODO is same as Sphingomonas aromaticivorans
         FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408 );
         FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344 );
         FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275 );