X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Fnhx%2FNHXtags.java;h=7cf98e666c46e9cadd132e8f0d7e000409e41d54;hb=6062dfb954cafb6af22e01af89222888d9d5ba66;hp=ae884abf236b155df19926bcb515c1741a13a4b6;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
index ae884ab..7cf98e6 100644
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,41 +15,23 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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.io.parsers.nhx;
 
 public final class NHXtags {
 
-    public static final String CUSTOM_DATA_ON_NODE        = "XN=";
-    public static final String COLOR                      = "C=";
-    public static final String PARENT_BRANCH_WIDTH        = "W=";
-    public static final String SUBTREE_NEIGHBORS          = "SNn=";
-    public static final String SUPER_ORTHOLOGOUS          = "SOn=";
-    public static final String ORTHOLOGOUS                = "On=";
-    public static final String TAXONOMY_ID                = "T=";
-    public static final String SUPPORT                    = "B=";
-    public static final String IS_DUPLICATION             = "D=";
-    public static final String ANNOTATION                 = "AN="; //TODO fix on website NHXv2
-    public static final String SPECIES_NAME               = "S=";
-    public static final String DOMAIN_STRUCTURE           = "DS=";
-    public static final String GENE_NAME                  = "GN=";
-    public static final String GENE_NAME_SYNONYM          = "G=";
-    public static final String SEQUENCE_ACCESSION         = "AC=";
-    public static final String NODE_IDENTIFIER            = "ID="; //TODO fix on website NHXv2
-    public static final Object BRANCH_WIDTH               = "W=";
-    @Deprecated
-    public static final String BINARY_DOMAIN_COMBINATIONS = "GDC=";
-    @Deprecated
-    public static final String DOMAINS_SEPARATOR          = "\\|";
-    @Deprecated
-    public static final String DOMAINS                    = "GD=";
-    @Deprecated
-    public static final String EC_NUMBER                  = "E=";
+    public static final String TAXONOMY_ID        = "T=";
+    public static final String SUPPORT            = "B=";
+    public static final String IS_DUPLICATION     = "D=";
+    public static final String SPECIES_NAME       = "S=";
+    public static final String DOMAIN_STRUCTURE   = "DS=";
+    public static final String GENE_NAME          = "GN=";
+    public static final String SEQUENCE_ACCESSION = "AC=";
 }