Class ParserUtils


  • public final class ParserUtils
    extends java.lang.Object
    • Field Detail

      • 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)
      • 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