- final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
- final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
- final static private String SDI_OPTION = "b";
- final static private String MOST_PARSIMONIOUS_OPTION = "m";
- final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml";
- final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
- final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
- final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
- final static private String PRG_NAME = "gsdi";
- final static private String PRG_VERSION = "0.901";
- final static private String PRG_DATE = "120608";
- final static private String PRG_DESC = "general speciation duplication inference";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "www.phylosoft.org/forester";
+ final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
+ final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
+ final static private String SDISE_OPTION = "b";
+ final static private String GSDIR_OPTION = "r";
+ final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
+ final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
+ final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt";
+ final static private String PRG_NAME = "gsdi";
+ final static private String PRG_VERSION = "1.000";
+ final static private String PRG_DATE = "120629";
+ final static private String PRG_DESC = "general speciation duplication inference";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "www.phylosoft.org/forester";