org.forester.io.parsers.nhx
public final class NHXParser extends java.lang.Object implements PhylogenyParser
Modifier and Type | Class and Description |
---|---|
static class |
NHXParser.TAXONOMY_EXTRACTION |
Modifier and Type | Field and Description |
---|---|
static boolean |
LIMIT_SPECIES_NAMES_TO_FIVE_CHARS |
static boolean |
REPLACE_UNDERSCORES_DEFAULT |
static NHXParser.TAXONOMY_EXTRACTION |
TAXONOMY_EXTRACTION_DEFAULT |
Constructor and Description |
---|
NHXParser() |
Modifier and Type | Method and Description |
---|---|
NHXParser.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,
NHXParser.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(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) |
public static final boolean LIMIT_SPECIES_NAMES_TO_FIVE_CHARS
public static final NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT
public static final boolean REPLACE_UNDERSCORES_DEFAULT
public NHXParser.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(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
public static void parseNHX(java.lang.String s, PhylogenyNode node_to_annotate, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores) throws NHXFormatException
NHXFormatException