- private static final String SEQUENCE_NAME_FIELD = "s";
- private static final String TAXONOMY_CODE_FIELD = "c";
- private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
- private static final String DS_FILED = "d";
- private static final String SEQUENCE_ANNOTATION_DESC = "a";
- private static final String NODE_NAME_FIELD = "n";
- final static private String PICKY_OPTION = "p";
- final static private String FIELD_OPTION = "f";
- final static private String TRIM_AFTER_TILDE_OPTION = "t";
- final static private String MOVE_DOMAIN_NUMBER_OPTION = "mdn"; // Hidden expert option.
- final static private String TREE_NAME_OPTION = "pn";
- final static private String TREE_ID_OPTION = "pi";
- final static private String TREE_DESC_OPTION = "pd";
- final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
- final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x";
- final static private String PROCESS_SIMILAR_TO_OPTION = "xs";
- final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
- final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r";
- final static private String ADVANCED_TABLE_OPTION = "table";
- final static private String KEY_COLUMN = "k";
- final static private String VALUE_COLUMN = "v";
- final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
- final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ": ";
- final static private String PRG_NAME = "decorator";
- final static private String PRG_VERSION = "1.11";
- final static private String PRG_DATE = "2012.09.15";
-
- private static void argumentsError() {
- System.out.println();
- System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
- + "[mapping table file] <phylogenies outfile>" );
- System.out.println();
- System.out.println( "options:" );
- System.out.println();
- System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
- System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
- System.out.println( " in phylogenies infile if not found (in map) otherwise" );
- System.out.println( " -p : picky, fails if node name not found in mapping table" );
- System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
- System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
- System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
- System.out.println();
- System.out.println();
- System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
- System.out.println();
- System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
- System.out.println( " " + SEQUENCE_ANNOTATION_DESC
- + " : sequence annotation description" );
- System.out.println( " " + DS_FILED + " : domain structure" );
- System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
- System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
- + ": taxonomy scientific name" );
- System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
- System.out.println( " -k=<n> : key column in mapping table (0 based)," );
- System.out.println( " names of the node to be decorated - default is 0" );
- System.out.println( " -v=<n> : value column in mapping table (0 based)," );
- System.out.println( " data which with to decorate - default is 1" );
- System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
- + " : to extract bracketed scientific names" );
- System.out.println( " -s=<c> : column separator in mapping file, default is \""
- + decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
- System.out.println( " -x : process name \"intelligently\" (only for -f=n)" );
- System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
- + " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
- System.out.println( " -c : cut name after first space (only for -f=n)" );
- System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
- + " : trim node name to be replaced after tilde" );
- System.out.println();
- System.exit( -1 );
- }
+ private static final String SEQUENCE_NAME_FIELD = "s";
+ private static final String MOL_SEQ = "m";
+ private static final String TAXONOMY_CODE_FIELD = "c";
+ private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
+ private static final String DS_FILED = "d";
+ private static final String SEQUENCE_ANNOTATION_DESC = "a";
+ private static final String NODE_NAME_FIELD = "n";
+ final static private String PICKY_OPTION = "p";
+ final static private String FIELD_OPTION = "f";
+ final static private String TRIM_AFTER_TILDE_OPTION = "t";
+ final static private String VERBOSE_OPTION = "ve";
+ final static private String TREE_NAME_OPTION = "pn";
+ final static private String TREE_ID_OPTION = "pi";
+ final static private String TREE_DESC_OPTION = "pd";
+ final static private String MIDPOINT_ROOT_OPTION = "mp";
+ final static private String ORDER_TREE_OPTION = "or";
+ final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
+ final static private String EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc";
+ final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
+ final static private String ADVANCED_TABLE_OPTION = "table";
+ final static private String KEY_COLUMN = "k";
+ final static private String VALUE_COLUMN = "v";
+ final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
+ final static private char MAPPING_FILE_SEPARATOR_DEFAULT = '\t';
+ final static private String PRG_NAME = "decorator";
+ final static private String PRG_VERSION = "1.16";
+ final static private String PRG_DATE = "131113";