public final class NHXParser implements PhylogenyParser {
- public static final boolean LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = true;
+ public static final boolean LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = false;
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;
isReplaceUnderscores() );
if ( NHXParser.GUESS_IF_SUPPORT_VALUES ) {
if ( NHXParser.isBranchLengthsLikeBootstrapValues( getCurrentPhylogeny() ) ) {
- NHXParser.moveBranchLengthsToBootstrapValues( getCurrentPhylogeny() );
+ NHXParser.moveBranchLengthsToConfidenceValues( getCurrentPhylogeny() );
}
}
if ( isGuessRootedness() ) {
&& ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
saw_colon = false;
}
- }
- if ( in_open_bracket && ( c == ']' ) ) {
- in_open_bracket = false;
+ if ( in_open_bracket && ( c == ']' ) ) {
+ in_open_bracket = false;
+ }
}
// \n\t is always ignored,
// as is " (34) and ' (39) (space is 32):
return true;
}
- private static void moveBranchLengthsToBootstrapValues( final Phylogeny p ) {
+ private static void moveBranchLengthsToConfidenceValues( final Phylogeny p ) {
final PhylogenyNodeIterator it = p.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();