Package org.forester.io.parsers.util

Class ParserUtils

java.lang.Object

org.forester.io.parsers.util.ParserUtils

public final class ParserUtils
extends java.lang.Object

Field Summary

Fields

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 Summary

Constructors

Constructor	Description
ParserUtils()

Method Summary

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)

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 java.lang.String TAX_CODE

See Also:

Constant Field Values

TAX_CODE_LO

public static final java.lang.String TAX_CODE_LO

See Also:

Constant Field Values

TAXOMONY_CODE_PATTERN_A

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A

TAXOMONY_CODE_PATTERN_A_LO

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A_LO

TAXOMONY_CODE_PATTERN_BRACKETED

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_BRACKETED

TAXOMONY_CODE_PATTERN_PFR

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_PFR

TAXOMONY_SN_PATTERN_GENUS

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_GENUS

TAXOMONY_SN_PATTERN_SN

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SN

TAXOMONY_SN_PATTERN_SNS

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS

TAXOMONY_SN_PATTERN_SNS2

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS2

TAXOMONY_SN_PATTERN_SP

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SP

TAXOMONY_SN_PATTERN_STRAIN_1

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_1

TAXOMONY_SN_PATTERN_STRAIN_2

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_2

TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

Constructor Detail

ParserUtils

public ParserUtils()

Method Detail

createParserDependingFileContents

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

Throws:

java.io.FileNotFoundException

java.io.IOException

createParserDependingOnFileType

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

Throws:

java.io.FileNotFoundException

java.io.IOException

createParserDependingOnUrlContents

public static final PhylogenyParser createParserDependingOnUrlContents(java.net.URL url,
                                                                       boolean phyloxml_validate_against_xsd)
                                                                throws java.io.FileNotFoundException,
                                                                       java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

createReader

public static java.io.BufferedReader createReader(java.lang.Object source)
                                           throws java.io.IOException,
                                                  java.io.FileNotFoundException

Throws:

java.io.IOException

java.io.FileNotFoundException

extractScientificNameFromNodeName

public static final java.lang.String extractScientificNameFromNodeName(java.lang.String name)

extractTaxonomyCodeFromNodeName

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

extractTaxonomyDataFromNodeName

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

Throws:

PhyloXmlDataFormatException

extractUniprotTaxonomyIdFromNodeName

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

readPhylogenies

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

Throws:

java.io.FileNotFoundException

java.io.IOException

readPhylogenies

public static final Phylogeny[] readPhylogenies(java.lang.String file_name)
                                         throws java.io.FileNotFoundException,
                                                java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException