X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterConstants.java;h=ffb6c96a09ef5ed0ffbd982848e0263f280b5f86;hb=eb22dac14771c467104f57362e3a624d0140f897;hp=3edec56f07ac01d0442adaeb86d4490ae0b517e2;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 3edec56..ffb6c96 100644
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2000-2009 Christian M. Zmasek
 // Copyright (C) 2007-2009 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
@@ -15,25 +15,42 @@
 // 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.util;
 
 public final class ForesterConstants {
 
-    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";
-    public final static String  XML_SCHEMA_INSTANCE         = "http://www.w3.org/2001/XMLSchema-instance";
-    public final static String  LOCAL_PHYLOXML_XSD_RESOURCE = "resources/phyloxml.xsd";
-    public final static String  PHYLO_XML_SUFFIX            = ".xml";
-    public final static String  UTF8                        = "UTF-8";
-    public final static String  PHYLO_XML_REFERENCE         = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356";
-    public final static boolean RELEASE                     = false;
+    public final static String  FORESTER_VERSION                 = "1.046";
+    public final static String  FORESTER_DATE                    = "170830";
+    public final static String  PHYLO_XML_VERSION                = "1.20";
+    public final static String  PHYLO_XML_LOCATION               = "http://www.phyloxml.org";
+    public final static String  PHYLO_XML_XSD                    = "phyloxml.xsd";
+    public final static String  XML_SCHEMA_INSTANCE              = "http://www.w3.org/2001/XMLSchema-instance";
+    public final static String  LOCAL_PHYLOXML_XSD_RESOURCE      = "resources/phyloxml.xsd";
+    public final static String  PHYLO_XML_SUFFIX                 = ".xml";
+    public final static String  ID_NORMALIZED_FASTA_FILE_SUFFIX  = "_ni.fasta";
+    public final static String  ID_NORMALIZED_NEXUS_FILE_SUFFIX  = "_ni.nexus";
+    public final static String  ID_NORMALIZED_PHYLIP_FILE_SUFFIX = "_ni.phylip";
+    public final static String  FASTA_FILE_SUFFIX                = ".fasta";
+    public final static String  NEXUS_FILE_SUFFIX                = ".nexus";
+    public final static String  PHYLIP_FILE_SUFFIX               = ".phylip";
+    public final static String  ID_MAP_FILE_SUFFIX               = ".nim";
+    public final static String  UTF_8                            = "UTF-8";
+    public final static String  ISO_8859_1                       = "ISO-8859-1";
+    public final static String  PHYLO_XML_REFERENCE              = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356";
+    public final static boolean RELEASE                          = false;
+
+    public enum PhylogeneticTreeFormats {
+                                         NH,
+                                         NHX,
+                                         NEXUS,
+                                         PHYLOXML
+    }
 }