Package org.forester.io.parsers.util
Class ParserUtils
- java.lang.Object
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- org.forester.io.parsers.util.ParserUtils
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public final class ParserUtils extends java.lang.Object
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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
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Constructor Summary
Constructors Constructor Description ParserUtils()
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Method Summary
All Methods Static Methods Concrete Methods 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)
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Field Detail
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TAX_CODE
public static final java.lang.String TAX_CODE
- See Also:
- Constant Field Values
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TAX_CODE_LO
public static final java.lang.String TAX_CODE_LO
- See Also:
- Constant Field Values
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TAXOMONY_CODE_PATTERN_A
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A
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TAXOMONY_CODE_PATTERN_A_LO
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A_LO
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TAXOMONY_CODE_PATTERN_BRACKETED
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_BRACKETED
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TAXOMONY_CODE_PATTERN_PFR
public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_PFR
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TAXOMONY_SN_PATTERN_GENUS
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_GENUS
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TAXOMONY_SN_PATTERN_SN
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SN
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TAXOMONY_SN_PATTERN_SNS
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS
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TAXOMONY_SN_PATTERN_SNS2
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS2
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TAXOMONY_SN_PATTERN_SP
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SP
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TAXOMONY_SN_PATTERN_STRAIN_1
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_1
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TAXOMONY_SN_PATTERN_STRAIN_2
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_2
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TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN
public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN
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Method Detail
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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
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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
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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
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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
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extractScientificNameFromNodeName
public static final java.lang.String extractScientificNameFromNodeName(java.lang.String name)
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extractTaxonomyCodeFromNodeName
public static final java.lang.String extractTaxonomyCodeFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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extractTaxonomyDataFromNodeName
public static final java.lang.String extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) throws PhyloXmlDataFormatException
- Throws:
PhyloXmlDataFormatException
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extractUniprotTaxonomyIdFromNodeName
public static final java.lang.String extractUniprotTaxonomyIdFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
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readPhylogenies
public static final Phylogeny[] readPhylogenies(java.io.File file) throws java.io.FileNotFoundException, java.io.IOException
- Throws:
java.io.FileNotFoundException
java.io.IOException
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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
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