public final class ForesterConstants {
- public final static String FORESTER_VERSION = "1.030";
- public final static String FORESTER_DATE = "140115";
- 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
+ NH,
+ NHX,
+ NEXUS,
+ PHYLOXML
}
}