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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
util
/
TaxonomyUtil.java
diff --git
a/forester/java/src/org/forester/util/TaxonomyUtil.java
b/forester/java/src/org/forester/util/TaxonomyUtil.java
index
496c939
..
ef38563
100644
(file)
--- 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 {
}
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" );
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( "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" );
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( "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" );
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( "ALIXX", "stramenopiles" );
put( "BLAHO", "stramenopiles" );
put( "BIGNA", "rhizaria" );
+ put( "RETFI", "rhizaria" );
put( "TRYB2", "excavata" );
put( "TRYCR", "excavata" );
put( "LEIMA", "excavata" );
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( "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 );
FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408 );
FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344 );
FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275 );