- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
- final static private String AV_GAPINESS_OPTION = "a";
- final static private String STEP_OPTION = "s";
- final static private String LENGTH_OPTION = "l";
- final static private String REALIGN_OPTION = "r";
- final static private String PATH_TO_MAFFT_OPTION = "mafft";
- final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
- final static private String PRG_NAME = "msa_compactor";
- final static private String PRG_DESC = "multiple sequnce aligment compactor";
- final static private String PRG_VERSION = "0.01";
- final static private String PRG_DATE = "140314";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.#" );
+ final private static NumberFormat NF_4 = new DecimalFormat( "0.####" );
+ static {
+ NF_1.setRoundingMode( RoundingMode.HALF_UP );
+ NF_4.setRoundingMode( RoundingMode.HALF_UP );
+ }
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String REMOVE_WORST_OFFENDERS_OPTION = "r";
+ final static private String AV_GAPINESS_OPTION = "g";
+ final static private String STEP_OPTION = "s";
+ final static private String LENGTH_OPTION = "l";
+ final static private String REALIGN_OPTION = "a";
+ final static private String INFO_ONLY_OPTION = "i";
+ //
+ final static private String STEP_FOR_DIAGNOSTICS_OPTION = "sd";
+ final static private String MIN_LENGTH_OPTION = "ml";
+ final static private String GAP_RATIO_LENGTH_OPTION = "gr";
+ final static private String REPORT_ENTROPY = "e";
+ final static private String OUTPUT_FORMAT_OPTION = "f";
+ final static private String OUTPUT_REMOVED_SEQS_OPTION = "ro";
+ final static private String MAFFT_OPTIONS = "mo";
+ final static private String PERFORM_PHYLOGENETIC_INFERENCE = "t";
+ //
+ final static private String PATH_TO_MAFFT_OPTION = "mafft";
+ final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
+ final static private String PRG_NAME = "msa_compactor";
+ final static private String PRG_DESC = "multiple sequence aligment compactor";
+ final static private String PRG_VERSION = "0.3";
+ final static private String PRG_DATE = "140508";
+ final static private String E_MAIL = "czmasek@sanfordburham.org";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";