Class PhylogenyDecorator


  • public final class PhylogenyDecorator
    extends java.lang.Object
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String decorate​(Phylogeny phylogeny, java.util.Map<java.lang.String,​java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)  
      static java.lang.String decorate​(Phylogeny phylogeny, java.util.Map<java.lang.String,​java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,​java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)  
      static void decorate​(Phylogeny phylogeny, java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.String>> map, boolean picky)  
      static java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.String>> parseMappingTable​(java.io.File mapping_table_file)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • decorate

        public static void decorate​(Phylogeny phylogeny,
                                    java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.String>> map,
                                    boolean picky)
                             throws java.lang.IllegalArgumentException,
                                    PhyloXmlDataFormatException
        Throws:
        java.lang.IllegalArgumentException
        PhyloXmlDataFormatException
      • decorate

        public static java.lang.String decorate​(Phylogeny phylogeny,
                                                java.util.Map<java.lang.String,​java.lang.String> map,
                                                PhylogenyDecorator.FIELD field,
                                                boolean extract_bracketed_scientific_name,
                                                boolean extract_bracketed_tax_code,
                                                boolean picky,
                                                java.util.Map<java.lang.String,​java.lang.String> intermediate_map,
                                                boolean cut_name_after_space,
                                                boolean trim_after_tilde,
                                                boolean verbose)
                                         throws java.lang.IllegalArgumentException,
                                                PhyloXmlDataFormatException
        Parameters:
        phylogeny -
        map - maps names (in phylogeny) to new values if intermediate_map is null otherwise maps intermediate value to new value
        field -
        picky -
        intermediate_map - maps name (in phylogeny) to a intermediate value
        Throws:
        java.lang.IllegalArgumentException
        PhyloXmlDataFormatException
      • parseMappingTable

        public static java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.String>> parseMappingTable​(java.io.File mapping_table_file)
                                                                                                                              throws java.io.IOException
        Throws:
        java.io.IOException