org.forester.io.parsers.util

Class ParserUtils

java.lang.Object

org.forester.io.parsers.util.ParserUtils

public final class ParserUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	TAX_CODE
static String	TAX_CODE_LO
static Pattern	TAXOMONY_CODE_PATTERN_A
static Pattern	TAXOMONY_CODE_PATTERN_A_LO
static Pattern	TAXOMONY_CODE_PATTERN_BRACKETED
static Pattern	TAXOMONY_CODE_PATTERN_PFR
static Pattern	TAXOMONY_SN_PATTERN_GENUS
static Pattern	TAXOMONY_SN_PATTERN_SN
static Pattern	TAXOMONY_SN_PATTERN_SNS
static Pattern	TAXOMONY_SN_PATTERN_SNS2
static Pattern	TAXOMONY_SN_PATTERN_SP
static Pattern	TAXOMONY_SN_PATTERN_STRAIN_1
static Pattern	TAXOMONY_SN_PATTERN_STRAIN_2
static Pattern	TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

Constructor Summary

Constructors

Constructor and Description
ParserUtils()

Method Summary

Modifier and Type	Method and Description
static PhylogenyParser	createParserDependingFileContents(File file, boolean phyloxml_validate_against_xsd)
static PhylogenyParser	createParserDependingOnFileType(File file, boolean phyloxml_validate_against_xsd)
static PhylogenyParser	createParserDependingOnUrlContents(URL url, boolean phyloxml_validate_against_xsd)
static BufferedReader	createReader(Object source)
static String	extractScientificNameFromNodeName(String name)
static String	extractTaxonomyCodeFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static String	extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static String	extractUniprotTaxonomyIdFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static Phylogeny[]	readPhylogenies(File file)
static Phylogeny[]	readPhylogenies(String file_name)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TAX_CODE

public static final String TAX_CODE

See Also:

Constant Field Values

TAX_CODE_LO

public static final String TAX_CODE_LO

See Also:

Constant Field Values

TAXOMONY_CODE_PATTERN_A

public static final Pattern TAXOMONY_CODE_PATTERN_A

TAXOMONY_CODE_PATTERN_A_LO

public static final Pattern TAXOMONY_CODE_PATTERN_A_LO

TAXOMONY_CODE_PATTERN_BRACKETED

public static final Pattern TAXOMONY_CODE_PATTERN_BRACKETED

TAXOMONY_CODE_PATTERN_PFR

public static final Pattern TAXOMONY_CODE_PATTERN_PFR

TAXOMONY_SN_PATTERN_GENUS

public static final Pattern TAXOMONY_SN_PATTERN_GENUS

TAXOMONY_SN_PATTERN_SN

public static final Pattern TAXOMONY_SN_PATTERN_SN

TAXOMONY_SN_PATTERN_SNS

public static final Pattern TAXOMONY_SN_PATTERN_SNS

TAXOMONY_SN_PATTERN_SNS2

public static final Pattern TAXOMONY_SN_PATTERN_SNS2

TAXOMONY_SN_PATTERN_SP

public static final Pattern TAXOMONY_SN_PATTERN_SP

TAXOMONY_SN_PATTERN_STRAIN_1

public static final Pattern TAXOMONY_SN_PATTERN_STRAIN_1

TAXOMONY_SN_PATTERN_STRAIN_2

public static final Pattern TAXOMONY_SN_PATTERN_STRAIN_2

TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

public static final Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

Constructor Detail

ParserUtils

public ParserUtils()

Method Detail

createParserDependingFileContents

public static final PhylogenyParser createParserDependingFileContents(File file,
                                                                      boolean phyloxml_validate_against_xsd)
                                                               throws FileNotFoundException,
                                                                      IOException

Throws:

FileNotFoundException

IOException

createParserDependingOnFileType

public static final PhylogenyParser createParserDependingOnFileType(File file,
                                                                    boolean phyloxml_validate_against_xsd)
                                                             throws FileNotFoundException,
                                                                    IOException

Throws:

FileNotFoundException

IOException

createParserDependingOnUrlContents

public static final PhylogenyParser createParserDependingOnUrlContents(URL url,
                                                                       boolean phyloxml_validate_against_xsd)
                                                                throws FileNotFoundException,
                                                                       IOException

Throws:

FileNotFoundException

IOException

createReader

public static BufferedReader createReader(Object source)
                                   throws IOException,
                                          FileNotFoundException

Throws:

IOException

FileNotFoundException

extractScientificNameFromNodeName

public static final String extractScientificNameFromNodeName(String name)

extractTaxonomyCodeFromNodeName

public static final String extractTaxonomyCodeFromNodeName(String name,
                                                           NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

extractTaxonomyDataFromNodeName

public static final String extractTaxonomyDataFromNodeName(PhylogenyNode node,
                                                           NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
                                                    throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

extractUniprotTaxonomyIdFromNodeName

public static final String extractUniprotTaxonomyIdFromNodeName(String name,
                                                                NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

readPhylogenies

public static final Phylogeny[] readPhylogenies(File file)
                                         throws FileNotFoundException,
                                                IOException

Throws:

FileNotFoundException

IOException

readPhylogenies

public static final Phylogeny[] readPhylogenies(String file_name)
                                         throws FileNotFoundException,
                                                IOException

Throws:

FileNotFoundException

IOException