- public static final boolean LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = true;
- public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
- final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
- final static private boolean GUESS_IF_SUPPORT_VALUES = true;
- final static private boolean IGNORE_QUOTES_DEFAULT = false;
- final static public boolean REPLACE_UNDERSCORES_DEFAULT = false;
- private boolean _saw_closing_paren;
- final static private byte STRING = 0;
- final static private byte STRING_BUFFER = 1;
- final static private byte CHAR_ARRAY = 2;
- final static private byte BUFFERED_READER = 3;
- private boolean _guess_rootedness;
- private boolean _has_next;
- private boolean _ignore_quotes;
- private byte _input_type;
- private int _source_length;
- private PhylogenyNode _current_node;
- private StringBuilder _current_anotation;
- private Object _nhx_source;
- private int _clade_level;
- private List<Phylogeny> _phylogenies;
- private Phylogeny _current_phylogeny;
- private PhylogenyMethods.TAXONOMY_EXTRACTION _taxonomy_extraction;
- private boolean _replace_underscores;
- public final static Pattern UC_LETTERS_NUMBERS_PATTERN = Pattern
- .compile( "^[A-Z0-9]+$" );
- public final static Pattern NUMBERS_ONLY_PATTERN = Pattern
- .compile( "^[0-9\\.]+$" );
- public final static Pattern MB_PROB_PATTERN = Pattern
- .compile( "prob=([^,]+)" );
- public final static Pattern MB_PROB_SD_PATTERN = Pattern
- .compile( "prob_stddev=([^,]+)" );
- public final static Pattern MB_BL_PATTERN = Pattern
- .compile( "length_median=([^,]+)" );
+ public static final TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = NHXParser.TAXONOMY_EXTRACTION.NO;
+ final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
+ final static private boolean GUESS_IF_SUPPORT_VALUES = true;
+ final static private boolean IGNORE_QUOTES_DEFAULT = false;
+ final static public boolean REPLACE_UNDERSCORES_DEFAULT = false;
+ private boolean _saw_closing_paren;
+ final static private byte STRING = 0;
+ final static private byte STRING_BUFFER = 1;
+ final static private byte CHAR_ARRAY = 2;
+ final static private byte BUFFERED_READER = 3;
+ private boolean _guess_rootedness;
+ private boolean _has_next;
+ private boolean _ignore_quotes;
+ private byte _input_type;
+ private int _source_length;
+ private PhylogenyNode _current_node;
+ private StringBuilder _current_anotation;
+ private Object _nhx_source;
+ private int _clade_level;
+ private List<Phylogeny> _phylogenies;
+ private Phylogeny _current_phylogeny;
+ private NHXParser.TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private boolean _replace_underscores;
+ public final static Pattern UC_LETTERS_NUMBERS_PATTERN = Pattern.compile( "^[A-Z0-9]+$" );
+ public final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
+ public final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([^,]+)" );
+ public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob_stddev=([^,]+)" );
+ public final static Pattern MB_BL_PATTERN = Pattern.compile( "length_median=([^,]+)" );