public final class ParserUtils
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
TAX_CODE |
|
static java.lang.String |
TAX_CODE_LO |
|
static java.util.regex.Pattern |
TAXOMONY_CODE_PATTERN_A |
|
static java.util.regex.Pattern |
TAXOMONY_CODE_PATTERN_A_LO |
|
static java.util.regex.Pattern |
TAXOMONY_CODE_PATTERN_BRACKETED |
|
static java.util.regex.Pattern |
TAXOMONY_CODE_PATTERN_PFR |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_GENUS |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_SN |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_SNS |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_SNS2 |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_SP |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_STRAIN_1 |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_STRAIN_2 |
|
static java.util.regex.Pattern |
TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN |
Constructor | Description |
---|---|
ParserUtils() |
Modifier and Type | Method | Description |
---|---|---|
static PhylogenyParser |
createParserDependingFileContents(java.io.File file,
boolean phyloxml_validate_against_xsd) |
|
static PhylogenyParser |
createParserDependingOnFileType(java.io.File file,
boolean phyloxml_validate_against_xsd) |
|
static PhylogenyParser |
createParserDependingOnUrlContents(java.net.URL url,
boolean phyloxml_validate_against_xsd) |
|
static java.io.BufferedReader |
createReader(java.lang.Object source) |
|
static java.lang.String |
extractScientificNameFromNodeName(java.lang.String name) |
|
static java.lang.String |
extractTaxonomyCodeFromNodeName(java.lang.String name,
NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) |
|
static java.lang.String |
extractTaxonomyDataFromNodeName(PhylogenyNode node,
NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) |
|
static java.lang.String |
extractUniprotTaxonomyIdFromNodeName(java.lang.String name,
NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) |
|
static Phylogeny[] |
readPhylogenies(java.io.File file) |
|
static Phylogeny[] |
readPhylogenies(java.lang.String file_name) |
public static final java.lang.String TAX_CODE
public static final java.lang.String TAX_CODE_LO
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A_LO
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_BRACKETED
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_PFR
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_GENUS
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SN
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS2
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SP
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_1
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_2
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN
public static final PhylogenyParser createParserDependingFileContents(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnFileType(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnUrlContents(java.net.URL url, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static java.io.BufferedReader createReader(java.lang.Object source) throws java.io.IOException, java.io.FileNotFoundException
java.io.IOException
java.io.FileNotFoundException
public static final java.lang.String extractScientificNameFromNodeName(java.lang.String name)
public static final java.lang.String extractTaxonomyCodeFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
public static final java.lang.String extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) throws PhyloXmlDataFormatException
PhyloXmlDataFormatException
public static final java.lang.String extractUniprotTaxonomyIdFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
public static final Phylogeny[] readPhylogenies(java.io.File file) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final Phylogeny[] readPhylogenies(java.lang.String file_name) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException