inprogress

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 97c04d3..ec4878c 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -215,8 +215,8 @@ public class surfacing {
     final static private String                               INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private String                               PRG_VERSION                                                                   = "2.303";
-    final static private String                               PRG_DATE                                                                      = "131022";
+    final static private String                               PRG_VERSION                                                                   = "2.304";
+    final static private String                               PRG_DATE                                                                      = "131024";
     final static private String                               E_MAIL                                                                        = "czmasek@burnham.org";
     final static private String                               WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 9f586d4..aeaa225 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                               // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9815 PD";
-    final static String         PRG_DATE                                                      = "130925";
+    final static String         VERSION                                                       = "0.9816 PD";
+    final static String         PRG_DATE                                                      = "131024";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java b/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java
new file mode 100644 (file)
index 0000000..d7090ad
--- /dev/null
+++ b/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java
@@ -0,0 +1,526 @@
+
+package org.forester.archaeopteryx;
+
+import java.util.HashMap;
+import java.util.Map;
+
+final class TaxonomyUtil {
+
+    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( "PANTR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "GORGO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PONAB", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "NOMLE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MACMU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PAPHA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CALJA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TARSY", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MICMU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "OTOGA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TUPBE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MOUSE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "RAT", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MESAU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "DIPOR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CAVPO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "HETGA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "SPETR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "OCHPR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "RABIT", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "BOVIN", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "SHEEP", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "BALMU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TURTR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PIG", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "LAMPA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "HORSE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MYOLU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PTEVA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "AILME", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CANFA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "FELCA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ERIEU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "SORAR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "LOXAF", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PROCA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ECHTE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CHOHO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "DASNO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MACEU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "SARHA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MONDO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ORNAN", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CHICK", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "MELGA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ANAPL", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TAEGU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ALLMI", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PELSI", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ANOCA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "XENLA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "XENTR", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "LATCH", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ORYLA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "XIPMA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "GASAC", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TAKRU", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "TETNG", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "ORENI", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "GADMO", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "DANRE", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CALMI", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "PETMA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CIOIN", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "CIOSA", "deuterostomia" );
+        _default_taxcode_taxgroup_map.put( "OIKDI", "deuterostomia" );
+        _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( "DROSE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROSI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROME", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROYA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROER", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROAN", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROPE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROPS", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROWI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROMO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROVI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DROGR", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "AEDAE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ANOGA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CULPI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "BOMMO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DANPL", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ATTCE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ACREC", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAMFO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "APIME", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "NASVI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "TRICA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ACYPI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "RHOPR", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "PEDHC", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ARTSF", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "DAPPU", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "HOMAM", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ANTGC", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "NARAN", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "SCUCO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "STRMM", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "IXOSC", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "TETUR", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "MESMA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "LIMPO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "HYPDU", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAEBR", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAERE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAEBE", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAEEL", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CAEJA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "PRIPA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "BRUMA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "WUCBA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "TRISP", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "APLCA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "LOTGI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CRAGI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "PINFU", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CTEXX", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "HELRO", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "SCHMA", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "CLOSI", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ECHMU", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "SCHMD", "protostomia" );
+        _default_taxcode_taxgroup_map.put( "ACRDI", "cnidaria" );
+        _default_taxcode_taxgroup_map.put( "NEMVE", "cnidaria" );
+        _default_taxcode_taxgroup_map.put( "HMAXX", "cnidaria" );
+        _default_taxcode_taxgroup_map.put( "TRIAD", "placozoa" );
+        _default_taxcode_taxgroup_map.put( "MNELE", "ctenophora" );
+        _default_taxcode_taxgroup_map.put( "AMPQE", "porifera" );
+        _default_taxcode_taxgroup_map.put( "MONBE", "choanoflagellida" );
+        _default_taxcode_taxgroup_map.put( "SALS5", "choanoflagellida" );
+        _default_taxcode_taxgroup_map.put( "AMOPA", "ichthyophonida & filasterea" );
+        _default_taxcode_taxgroup_map.put( "SARXX", "ichthyophonida & filasterea" );
+        _default_taxcode_taxgroup_map.put( "CAPO3", "ichthyophonida & filasterea" );
+        _default_taxcode_taxgroup_map.put( "AALXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "GIBZE", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "HYPVG", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MAGGR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "THIHA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "THITE", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CHAGB", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "NEUCR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "BOTF4", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SCLS1", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PFIXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MYCGM", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MYCPJ", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MPSXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "BCOXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "APPXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "APMXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "APSXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "COCSA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SETTU", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PYRTR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PHANO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "ASPFN", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "ASPNC", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "ASPCL", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "EMENI", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "NEOFI", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "COCIM", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "UNCRE", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "AJECG", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "TUBMM", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "NAUCC", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "YEAST", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "KLULA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "ASHGO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CANAL", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CANTT", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "DEBHA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "YARLI", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SCHJY", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SCHOT", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SCHPO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PNECA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "AGABU", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "COPC7", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "LACBS", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PLEOS", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CPUXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SERL9", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "JARXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "GLOTR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "FPIXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PPLXX", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "TRAVE", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "WOLCO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CERSU", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "DICSQ", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "HETAN", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "CRYNE", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "TREME", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MALGO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "USTMA", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MELLP", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "PUCGR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "RHOGR", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "SPORO", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "WALSC", "dikarya" );
+        _default_taxcode_taxgroup_map.put( "MUCCI", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "PHYBL", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "RHIOR", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "MVNXX", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "CREXX", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "ALLMA", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "BATDJ", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "SPIPN", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "GONPR", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "PIRSE", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "ENCCU", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "ENCHA", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "VITCO", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "ENTBH", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "TRAHO", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "VAVCU", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "EDHAE", "other fungi" );
+        _default_taxcode_taxgroup_map.put( "FALXX", "nucleariidae and fonticula group" );
+        _default_taxcode_taxgroup_map.put( "DICDI", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "DICPU", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "DICFS", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "POLPA", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "ENTHI", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "ENTDS", "amoebozoa" );
+        _default_taxcode_taxgroup_map.put( "FRAVE", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "PRUPE", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "CUCSA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SOYBN", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "MEDTR", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "MANES", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "RICCO", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "POPTR", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "ARALY", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "ARATH", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "THEHA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "CARPA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "CCLXX", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "CITSI", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "EUCGR", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "VITVI", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SOLLC", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SOLPI", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SOLTU", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "TOBAC", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "MIMGU", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "AQUCA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SORBI", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "MAIZE", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "PANVG", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "SETIT", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "ORYSA", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "ORYSJ", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "BRADI", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "HORVD", "embryophyta" );
+        _default_taxcode_taxgroup_map.put( "MUSAM", "embryophyta" );
+        _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( "OSTLU", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "ORCXX", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "OSTTA", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "MICPC", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "MICSR", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "ASCXX", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "CHLVA", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "CSUXX", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "CHLRE", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "VOLCA", "chlorophyta" );
+        _default_taxcode_taxgroup_map.put( "CYAME", "rhodophyta" );
+        _default_taxcode_taxgroup_map.put( "GALSU", "rhodophyta" );
+        _default_taxcode_taxgroup_map.put( "CHOCR", "rhodophyta" );
+        _default_taxcode_taxgroup_map.put( "CYAPA", "glaucocystophyceae" );
+        _default_taxcode_taxgroup_map.put( "EMIHU", "hacrobia" );
+        _default_taxcode_taxgroup_map.put( "GUITH", "hacrobia" );
+        _default_taxcode_taxgroup_map.put( "PLACH", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "PLAF7", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "PLAYO", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "PLAVS", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "THEAN", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "THEPA", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "BABBO", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "EIMTE", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "TOXGO", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "CRYHO", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "CRYPV", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "CRYPI", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "CRYCO", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "THOHE", "alveolata" );
+        _default_taxcode_taxgroup_map.put( "PARTE", "alveolata" );
+        _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( "FCYXX", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHATR", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "THAPS", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "THAOC", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "AURAN", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "ECTSI", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHYIN", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHYRM", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHYSO", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHYCI", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PHYCP", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "HYAAE", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "PYTUL", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "AKEXX", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "SAGXX", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "ALIXX", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "BLAHO", "stramenopiles" );
+        _default_taxcode_taxgroup_map.put( "BIGNA", "rhizaria" );
+        _default_taxcode_taxgroup_map.put( "TRYB2", "excavata" );
+        _default_taxcode_taxgroup_map.put( "TRYCR", "excavata" );
+        _default_taxcode_taxgroup_map.put( "LEIMA", "excavata" );
+        _default_taxcode_taxgroup_map.put( "LEIIN", "excavata" );
+        _default_taxcode_taxgroup_map.put( "LEIBR", "excavata" );
+        _default_taxcode_taxgroup_map.put( "BODSA", "excavata" );
+        _default_taxcode_taxgroup_map.put( "NAEGR", "excavata" );
+        _default_taxcode_taxgroup_map.put( "GIAIC", "excavata" );
+        _default_taxcode_taxgroup_map.put( "TRIVA", "excavata" );
+        _default_taxcode_taxgroup_map.put( "TTRXX", "apusozoa" );
+        _default_taxcode_taxgroup_map.put( "METAC", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METBF", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METMA", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METBU", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METB6", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METHU", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METMJ", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METLZ", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METTP", "archaea" );
+        _default_taxcode_taxgroup_map.put( "HALMA", "archaea" );
+        _default_taxcode_taxgroup_map.put( "NATPH", "archaea" );
+        _default_taxcode_taxgroup_map.put( "HALS3", "archaea" );
+        _default_taxcode_taxgroup_map.put( "HALSP", "archaea" );
+        _default_taxcode_taxgroup_map.put( "HALWD", "archaea" );
+        _default_taxcode_taxgroup_map.put( "ARCFU", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METJA", "archaea" );
+        _default_taxcode_taxgroup_map.put( "META3", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METMP", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METVS", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METS3", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METST", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METTH", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METKA", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRFU", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRKO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRAB", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRHO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "THEON", "archaea" );
+        _default_taxcode_taxgroup_map.put( "NANEQ", "archaea" );
+        _default_taxcode_taxgroup_map.put( "NITMS", "archaea" );
+        _default_taxcode_taxgroup_map.put( "THEAC", "archaea" );
+        _default_taxcode_taxgroup_map.put( "THEVO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PICTO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRAR", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRCJ", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRAE", "archaea" );
+        _default_taxcode_taxgroup_map.put( "PYRIL", "archaea" );
+        _default_taxcode_taxgroup_map.put( "THENV", "archaea" );
+        _default_taxcode_taxgroup_map.put( "CALMQ", "archaea" );
+        _default_taxcode_taxgroup_map.put( "SULAC", "archaea" );
+        _default_taxcode_taxgroup_map.put( "SULTO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "SULSO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "METS5", "archaea" );
+        _default_taxcode_taxgroup_map.put( "AERPE", "archaea" );
+        _default_taxcode_taxgroup_map.put( "STAMF", "archaea" );
+        _default_taxcode_taxgroup_map.put( "THEPD", "archaea" );
+        _default_taxcode_taxgroup_map.put( "HYPBU", "archaea" );
+        _default_taxcode_taxgroup_map.put( "IGNH4", "archaea" );
+        _default_taxcode_taxgroup_map.put( "KORCO", "archaea" );
+        _default_taxcode_taxgroup_map.put( "ECOLI", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ECO57", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SHIFL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SALTY", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "YERPE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PHOLU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PHOPR", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "VIBCH", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SHEDO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PSEF5", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PSEPF", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PSEAE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHRSD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DECAR", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RALME", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NITEU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NITMU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THIDE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ALHEH", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "HALHL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NITOC", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THICR", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "IDILO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "LEGPN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "XANAC", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "XYLFT", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "AGRT5", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHIEC", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BRAJA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHOPT", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHOS1", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ROSDO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CAUCR", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ACICY", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHORU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "HAEIN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PASMU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NEIME", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ACIFE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DESPS", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DESDE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SYNAS", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "GEOME", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "GEOSL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ANADE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MYXXA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ACIBL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SOLUS", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHOBA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "KINRD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "KOCRD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MICPN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "STRCO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THEFY", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MYCLE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MYCTU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CORJK", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RHOOB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RUBXD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLAU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ROSCS", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "HERAU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SPHTD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DEIGD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DEIRA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THET8", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ANAVT", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NOSS7", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NOSP7", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "ACAM1", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MICAN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "TRIER", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SYNEL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SYNY3", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "GLOVI", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PROMA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PROMP", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PROMM", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SYNS3", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLPB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PROAE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PELLU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PROVI", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLP8", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLTE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLCH", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLTA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "FLAJO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "GRAFK", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CYTH3", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACFR", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACTN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PORGI", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SALRD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "AKKM8", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "METI4", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "LEPIC", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACAN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACC3", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACSU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BACHD", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "GEOKA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "LISMO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "STAAU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CLOP1", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CARHZ", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THETN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DESHA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "EUBR3", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "FERNB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THELT", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "THEMA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MYCGE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MYCPN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "MESFL", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "UREPA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BORBU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "TREPA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLPN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLFF", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CHLMU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RICTY", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BARHE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "PELUB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RICB8", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "RICRO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "FRATU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "STRPN", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "STRPY", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "LACLA", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "LACAC", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "BIFLO", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "FUSNU", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DEHE1", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "DEHSB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "NITSB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "SULNB", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "CAMJE", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "HELPH", "bacteria" );
+        _default_taxcode_taxgroup_map.put( "AQUAE", "bacteria" );
+    }
+}

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 73544b7..f23f865 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -2257,7 +2257,10 @@ public final class SurfacingUtil {
             writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
             writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
             writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
-            writeColorLabels( "Fungi", TaxonomyColors.FUNGI_COLOR, w );
+            writeColorLabels( "Dikarya (Ascomycota & Basidiomycota, so-called \"higher fungi\")",
+                              TaxonomyColors.DIKARYA_COLOR,
+                              w );
+            writeColorLabels( "other Fungi", TaxonomyColors.OTHER_FUNGI_COLOR, w );
             writeColorLabels( "Nucleariidae and Fonticula group",
                               TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
                               w );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 66bff3d..a57974a 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -2776,7 +2776,7 @@ public final class Test {
 
     private static boolean testTreeCopy() {
         try {
-            final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])";
+            final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
             final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
             final Phylogeny t1 = t0.copy();
             if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
@@ -2787,14 +2787,16 @@ public final class Test {
             }
             t0.deleteSubtree( t0.getNode( "c" ), true );
             t0.deleteSubtree( t0.getNode( "a" ), true );
-            t0.deleteSubtree( t0.getNode( "e" ), true );
-            if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" ) ) {
+            t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
+            t0.getNode( "b" ).setName( "Bee" );
+            if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
                 return false;
             }
             if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
-            t0.deleteSubtree( t0.getNode( "b" ), true );
+            t0.deleteSubtree( t0.getNode( "e" ), true );
+            t0.deleteSubtree( t0.getNode( "Bee" ), true );
             t0.deleteSubtree( t0.getNode( "d" ), true );
             if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 3364ddb..bd601f7 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.028";
-    public final static String  FORESTER_DATE               = "130528";
+    public final static String  FORESTER_VERSION            = "1.029";
+    public final static String  FORESTER_DATE               = "131024";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index b819971..eef965f 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -1240,9 +1240,13 @@ public final class ForesterUtil {
             printRel( tax_code, "ichthyophonida & filasterea" );
             return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
         }
-        else if ( tax.equalsIgnoreCase( "fungi" ) ) {
-            printRel( tax_code, "fungi" );
-            return TaxonomyColors.FUNGI_COLOR;
+        else if ( tax.equalsIgnoreCase( "dikarya" ) ) {
+            printRel( tax_code, "dikarya" );
+            return TaxonomyColors.DIKARYA_COLOR;
+        }
+        else if ( tax.equalsIgnoreCase( "fungi" ) || tax.equalsIgnoreCase( "other fungi" ) ) {
+            printRel( tax_code, "other fungi" );
+            return TaxonomyColors.OTHER_FUNGI_COLOR;
         }
         else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
             printRel( tax_code, "nucleariidae and fonticula group" );
@@ -1305,6 +1309,6 @@ public final class ForesterUtil {
 
     private final static void printRel( final String tax_code, final String group ) {
         //System.out.println( tax_code + "->" + group );
-        System.out.println( "_default_taxcode_taxgroup_map.put( \"" + tax_code + "\", \"" + group + "\" );" );
+        //System.out.println( "_default_taxcode_taxgroup_map.put( \"" + tax_code + "\", \"" + group + "\" );" );
     }
 }

diff --git a/forester/java/src/org/forester/util/TaxonomyColors.java b/forester/java/src/org/forester/util/TaxonomyColors.java
index 1a3bdb4..8890865 100644 (file)
--- a/forester/java/src/org/forester/util/TaxonomyColors.java
+++ b/forester/java/src/org/forester/util/TaxonomyColors.java
@@ -2,36 +2,31 @@
 package org.forester.util;\r
 \r
 import java.awt.Color;\r
-import java.util.HashMap;\r
-import java.util.Map;\r
 \r
 public final class TaxonomyColors {\r
 \r
-    public final static Color                DEUTEROSTOMIA_COLOR                    = new Color( 255, 0, 0 );\r
-    public final static Color                PROTOSTOMIA_COLOR                      = new Color( 204, 0, 0 );\r
-    public final static Color                CNIDARIA_COLOR                         = new Color( 204, 0, 142 );\r
-    public final static Color                PLACOZOA_COLOR                         = new Color( 204, 0, 132 );\r
-    public final static Color                CTENOPHORA_COLOR                       = new Color( 204, 0, 122 );\r
-    public final static Color                PORIFERA_COLOR                         = new Color( 204, 0, 112 );\r
-    public final static Color                CHOANOFLAGELLIDA                       = new Color( 135, 0, 255 );\r
-    public final static Color                ICHTHYOSPOREA_AND_FILASTEREA           = new Color( 125, 0, 225 );\r
-    public final static Color                FUNGI_COLOR                            = new Color( 255, 153, 0 );\r
-    public final static Color                NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR = new Color( 204, 102, 0 );\r
-    public final static Color                AMOEBOZOA_COLOR                        = new Color( 255, 0, 255 );\r
-    public final static Color                EMBRYOPHYTA_COLOR                      = new Color( 0, 255, 0 );\r
-    public final static Color                CHLOROPHYTA_COLOR                      = new Color( 0, 204, 0 );\r
-    public final static Color                RHODOPHYTA_COLOR                       = new Color( 0, 153, 76 );\r
-    public final static Color                HACROBIA_COLOR                         = new Color( 0, 90, 40 );\r
-    public final static Color                GLAUCOPHYTA_COLOR                      = new Color( 0, 90, 60 );\r
-    public final static Color                STRAMENOPILES_COLOR                    = new Color( 0, 0, 255 );\r
-    public final static Color                ALVEOLATA_COLOR                        = new Color( 0, 128, 255 );\r
-    public final static Color                RHIZARIA_COLOR                         = new Color( 0, 255, 255 );\r
-    public static final Color                APUSOZOA_COLOR                         = new Color( 204, 245, 245 );\r
-    public final static Color                EXCAVATA_COLOR                         = new Color( 204, 204, 0 );\r
-    public final static Color                ARCHAEA_COLOR                          = new Color( 160, 160, 160 );\r
-    public final static Color                BACTERIA_COLOR                         = new Color( 64, 64, 64 );\r
-    private final static Map<String, String> _default_taxcode_taxgroup_map          = new HashMap<String, String>();\r
-    static {\r
-        // _default_taxcode_taxgroup_map.put( key, value );\r
-    }\r
+    public final static Color DEUTEROSTOMIA_COLOR                    = new Color( 255, 0, 0 );\r
+    public final static Color PROTOSTOMIA_COLOR                      = new Color( 204, 0, 0 );\r
+    public final static Color CNIDARIA_COLOR                         = new Color( 204, 0, 142 );\r
+    public final static Color PLACOZOA_COLOR                         = new Color( 204, 0, 132 );\r
+    public final static Color CTENOPHORA_COLOR                       = new Color( 204, 0, 122 );\r
+    public final static Color PORIFERA_COLOR                         = new Color( 204, 0, 112 );\r
+    public final static Color CHOANOFLAGELLIDA                       = new Color( 135, 0, 255 );\r
+    public final static Color ICHTHYOSPOREA_AND_FILASTEREA           = new Color( 125, 0, 225 );\r
+    public final static Color DIKARYA_COLOR                          = new Color( 255, 155, 0 );\r
+    public final static Color OTHER_FUNGI_COLOR                      = new Color( 227, 127, 0 );\r
+    public final static Color NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR = new Color( 200, 100, 0 );\r
+    public final static Color AMOEBOZOA_COLOR                        = new Color( 255, 0, 255 );\r
+    public final static Color EMBRYOPHYTA_COLOR                      = new Color( 0, 255, 0 );\r
+    public final static Color CHLOROPHYTA_COLOR                      = new Color( 0, 204, 0 );\r
+    public final static Color RHODOPHYTA_COLOR                       = new Color( 0, 153, 76 );\r
+    public final static Color HACROBIA_COLOR                         = new Color( 0, 90, 40 );\r
+    public final static Color GLAUCOPHYTA_COLOR                      = new Color( 0, 90, 60 );\r
+    public final static Color STRAMENOPILES_COLOR                    = new Color( 0, 0, 255 );\r
+    public final static Color ALVEOLATA_COLOR                        = new Color( 0, 128, 255 );\r
+    public final static Color RHIZARIA_COLOR                         = new Color( 0, 255, 255 );\r
+    public static final Color APUSOZOA_COLOR                         = new Color( 204, 245, 245 );\r
+    public final static Color EXCAVATA_COLOR                         = new Color( 204, 204, 0 );\r
+    public final static Color ARCHAEA_COLOR                          = new Color( 160, 160, 160 );\r
+    public final static Color BACTERIA_COLOR                         = new Color( 64, 64, 64 );\r
 }\r