public final class NHXParser extends java.lang.Object implements PhylogenyParser
Modifier and Type | Field and Description |
---|---|
static java.util.regex.Pattern |
MB_BL_PATTERN |
static java.util.regex.Pattern |
MB_PROB_PATTERN |
static java.util.regex.Pattern |
MB_PROB_SD_PATTERN |
static java.util.regex.Pattern |
NUMBERS_ONLY_PATTERN |
static boolean |
REPLACE_UNDERSCORES_DEFAULT |
static PhylogenyMethods.TAXONOMY_EXTRACTION |
TAXONOMY_EXTRACTION_DEFAULT |
static java.util.regex.Pattern |
UC_LETTERS_NUMBERS_PATTERN |
Constructor and Description |
---|
NHXParser() |
Modifier and Type | Method and Description |
---|---|
PhylogenyMethods.TAXONOMY_EXTRACTION |
getTaxonomyExtraction() |
boolean |
hasNext() |
Phylogeny[] |
parse()
Parses the source set with setSource( final Object nhx_source ).
|
Phylogeny |
parseNext() |
static void |
parseNHX(java.lang.String s,
PhylogenyNode node_to_annotate,
PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
boolean replace_underscores) |
void |
setGuessRootedness(boolean guess_rootedness) |
void |
setIgnoreQuotes(boolean ignore_quotes) |
void |
setReplaceUnderscores(boolean replace_underscores) |
void |
setSource(java.lang.Object nhx_source)
This sets the source to be parsed.
|
void |
setTaxonomyExtraction(PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction) |
public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT
public static final boolean REPLACE_UNDERSCORES_DEFAULT
public static final java.util.regex.Pattern UC_LETTERS_NUMBERS_PATTERN
public static final java.util.regex.Pattern NUMBERS_ONLY_PATTERN
public static final java.util.regex.Pattern MB_PROB_PATTERN
public static final java.util.regex.Pattern MB_PROB_SD_PATTERN
public static final java.util.regex.Pattern MB_BL_PATTERN
public PhylogenyMethods.TAXONOMY_EXTRACTION getTaxonomyExtraction()
public boolean hasNext()
public Phylogeny[] parse() throws java.io.IOException, NHXFormatException
parse
in interface PhylogenyParser
java.io.IOException
NHXFormatException
PhylogenyParserException
#setSource( final Object nhx_source )
,
PhylogenyParser.parse()
public Phylogeny parseNext() throws java.io.IOException, NHXFormatException
java.io.IOException
NHXFormatException
public void setGuessRootedness(boolean guess_rootedness)
public void setIgnoreQuotes(boolean ignore_quotes)
public void setReplaceUnderscores(boolean replace_underscores)
public void setSource(java.lang.Object nhx_source) throws PhylogenyParserException, java.io.IOException
setSource
in interface PhylogenyParser
nhx_source
- the source to be parsed (String, StringBuffer, char[], File,
or InputStream)java.io.IOException
PhylogenyParserException
parse()
,
PhylogenyParser.setSource(java.lang.Object)
public void setTaxonomyExtraction(PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction)
public static void parseNHX(java.lang.String s, PhylogenyNode node_to_annotate, PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores) throws NHXFormatException, PhyloXmlDataFormatException