Package org.forester.io.parsers.util
Class ParserUtils
java.lang.Object
org.forester.io.parsers.util.ParserUtils
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final Stringstatic final Stringstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Patternstatic final Pattern -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final PhylogenyParsercreateParserDependingFileContents(File file, boolean phyloxml_validate_against_xsd) static final PhylogenyParsercreateParserDependingOnFileType(File file, boolean phyloxml_validate_against_xsd) static final PhylogenyParsercreateParserDependingOnUrlContents(URL url, boolean phyloxml_validate_against_xsd) static BufferedReadercreateReader(Object source) static final Stringstatic final StringextractTaxonomyCodeFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static final StringextractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static final StringextractUniprotTaxonomyIdFromNodeName(String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static final Phylogeny[]readPhylogenies(File file) static final Phylogeny[]readPhylogenies(String file_name)
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Field Details
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TAX_CODE
- See Also:
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TAX_CODE_LO
- See Also:
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TAXOMONY_CODE_PATTERN_A
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TAXOMONY_CODE_PATTERN_A_LO
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TAXOMONY_CODE_PATTERN_BRACKETED
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TAXOMONY_CODE_PATTERN_PFR
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TAXOMONY_SN_PATTERN_GENUS
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TAXOMONY_SN_PATTERN_SN
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TAXOMONY_SN_PATTERN_SNS
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TAXOMONY_SN_PATTERN_SNS2
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TAXOMONY_SN_PATTERN_SP
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TAXOMONY_SN_PATTERN_STRAIN_1
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TAXOMONY_SN_PATTERN_STRAIN_2
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TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN
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Constructor Details
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ParserUtils
public ParserUtils()
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Method Details
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createParserDependingFileContents
public static final PhylogenyParser createParserDependingFileContents(File file, boolean phyloxml_validate_against_xsd) throws FileNotFoundException, IOException - Throws:
FileNotFoundExceptionIOException
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createParserDependingOnFileType
public static final PhylogenyParser createParserDependingOnFileType(File file, boolean phyloxml_validate_against_xsd) throws FileNotFoundException, IOException - Throws:
FileNotFoundExceptionIOException
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createParserDependingOnUrlContents
public static final PhylogenyParser createParserDependingOnUrlContents(URL url, boolean phyloxml_validate_against_xsd) throws FileNotFoundException, IOException - Throws:
FileNotFoundExceptionIOException
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createReader
- Throws:
IOExceptionFileNotFoundException
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extractScientificNameFromNodeName
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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
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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:
FileNotFoundExceptionIOException
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readPhylogenies
public static final Phylogeny[] readPhylogenies(String file_name) throws FileNotFoundException, IOException - Throws:
FileNotFoundExceptionIOException
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