IteratingPhylogenyParser
, PhylogenyParser
public final class NHXParser extends java.lang.Object implements PhylogenyParser, IteratingPhylogenyParser
Modifier and Type | Class | Description |
---|---|---|
static class |
NHXParser.TAXONOMY_EXTRACTION |
Modifier and Type | Field | 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 |
Constructor | Description |
---|---|
NHXParser() |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getName() |
|
NHXParser.TAXONOMY_EXTRACTION |
getTaxonomyExtraction() |
|
boolean |
hasNext() |
|
Phylogeny |
next() |
|
Phylogeny[] |
parse() |
|
static Phylogeny[] |
parse(java.lang.Object nhx_source) |
|
static void |
parseNHX(java.lang.String s,
PhylogenyNode node_to_annotate,
NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
boolean replace_underscores,
boolean allow_errors_in_distance_to_parent,
boolean replace_bell) |
|
void |
reset() |
|
void |
setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent) |
|
void |
setGuessRootedness(boolean guess_rootedness) |
|
void |
setIgnoreQuotes(boolean ignore_quotes) |
|
void |
setReplaceUnderscores(boolean replace_underscores) |
|
void |
setSource(java.lang.Object nhx_source) |
|
void |
setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) |
public static final java.util.regex.Pattern MB_BL_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 NUMBERS_ONLY_PATTERN
public static final boolean REPLACE_UNDERSCORES_DEFAULT
public java.lang.String getName()
getName
in interface PhylogenyParser
public final NHXParser.TAXONOMY_EXTRACTION getTaxonomyExtraction()
public final boolean hasNext()
hasNext
in interface IteratingPhylogenyParser
public final Phylogeny next() throws NHXFormatException, java.io.IOException
next
in interface IteratingPhylogenyParser
NHXFormatException
java.io.IOException
public final Phylogeny[] parse() throws java.io.IOException
parse
in interface PhylogenyParser
java.io.IOException
public final void reset() throws NHXFormatException, java.io.IOException
reset
in interface IteratingPhylogenyParser
NHXFormatException
java.io.IOException
public final void setGuessRootedness(boolean guess_rootedness)
public final void setIgnoreQuotes(boolean ignore_quotes)
public final void setReplaceUnderscores(boolean replace_underscores)
public final void setSource(java.lang.Object nhx_source) throws NHXFormatException, java.io.IOException
setSource
in interface IteratingPhylogenyParser
setSource
in interface PhylogenyParser
NHXFormatException
java.io.IOException
public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
public final void setAllowErrorsInDistanceToParent(boolean allow_errors_in_distance_to_parent)
public static final Phylogeny[] parse(java.lang.Object nhx_source) throws NHXFormatException, java.io.IOException
NHXFormatException
java.io.IOException
public static final void parseNHX(java.lang.String s, PhylogenyNode node_to_annotate, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores, boolean allow_errors_in_distance_to_parent, boolean replace_bell) throws NHXFormatException, PhyloXmlDataFormatException