test_class.file: singa-sequence/src/test/java/bio/singa/sequence/parser/ena/ENAParserServiceTest.java
test_class.identifier: ENAParserServiceTest
test_case.body: @Test
      void shouldParseNucleotideSequence() {
          // parse sequence
          SequenceContainer sequenceContainer = ENAParserService.parseGeneTranslationPair(new ENAAccessionNumber("CAA37856.1"));
          NucleotideSequence gene = sequenceContainer.getGene();
          ProteinSequence translation = sequenceContainer.getTranslation();
  
          // compare gene
          assertEquals("ATGCGTACAGAATATTGTGGACAGCTCCGTTTGTCCCACGTGGGGCAGCAGGTGACTCTGTGTGGTTGGGTCAACCGTCGTCGTGAT" +
                  "CTTGGTAGCCTGATCTTCATCGATATGCGCGACCGCGAAGGTATCGTGCAGGTATTTTTCGATCCGGATCGTGCGGACGCGTTAAAGCTGGCCTCTGAAC" +
                  "TGCGTAATGAGTTCTGCATTCAGGTCACGGGCACCGTACGTGCGCGTGACGAAAAAAATATTAACCGCGATATGGCGACCGGCGAAATCGAAGTGCTGGC" +
                  "GTCCTCGCTGACTATCATCAACCGCGCAGATGTTCTGCCGCTTGACTCTAACCACGTCAACACCGAAGAAGCGCGTCTGAAATACCGCTACCTCGACCTG" +
                  "CGTCGTCCGGAAATGGCTCAGCGCCTGAAAACCCGCGCTAAAATCACCAGCCTGGTGCGCCGTTTTATGGATGACCACGGCTTCCTCGACATCGAAACTC" +
                  "CGATGCTGACCAAAGCCACGCCGGAAGGCGCGCGTGACTACCTGGTGCCTTCTCGTGTGCACAAAGGTAAATTCTACGCACTGCCGCAATCCCCGCAGTT" +
                  "GTTCAAACAGCTGCTGATGATGTCCGGTTTTGACCGTTACTATCAGATCGTTAAATGCTTCCGTGACGAAGACCTGCGTGCTGACCGTCAGCCTGAATTT" +
                  "ACTCAGATCGATGTGGAAACTTCTTTCATGACCGCGCCGCAAGTGCGTGAAGTGATGGAAGCGCTGGTGCGTCATCTGTGGCTGGAAGTGAAGGGTGTGG" +
                  "ATCTGGGCGATTTCCCGGTAATGACCTTTGCGGAAGCAGAACGCCGTTATGGTTCTGATAAACCGGATCTGCGTAACCCGATGGAACTGACTGACGTTGC" +
                  "TGATCTGCTGAAATCTGTTGAGTTTGCTGTATTTGCAGGTCCGGCGAACGATCCGAAAGGTCGCGTAGCGGCTCTGCGCGTTCCGGGCGGCGCATCGCTG" +
                  "ACCCGTAAGCAGATCGACGAATACGGTAACTTCGTTAAAATCTACGGCGCGAAAGGTCTGGCTTACATCAAAGTTAACGAACGCGCGAAAGGTCTGGAAG" +
                  "GTATCAACAGCCCGGTAGCGAAGTTCCTTAATGCAGAAATCATCGAAGACATCCTGGATCGTACTGCCGCGCAAGATGGCGATATGATTTTCTTCGGTGC" +
                  "CGACAACAAGAAAATTGTTGCCGACGCGATGGGTGCACTGCGCCTGAAAGTGGGTAAAGACCTTGGTCTGACCGACGAAAGCAAATGGGCACCGCTGTGG" +
                  "GTTATCGACTTCCCGATGTTTGAAGACGACGGTGAAGGCGGCCTGACGGCAATGCACCATCCGTTCACCTCACCGAAAGATATGACGGCTGCAGAACTGA" +
                  "AAGCTGCACCGGAAAATGCGGTGGCGAACGCTTACGATATGGTCATCAATGGTTACGAAGTGGGCGGTGGTTCAGTACGTATCCATAATGGTGATATGCA" +
                  "GCAGACGGTGTTTGGTATTCTGGGTATCAACGAAGAGGAACAGCGCGAGAAATTCGGCTTCCTGCTCGACGCTCTGAAATACGGTACTCCGCCGCACGCA" +
                  "GGTCTGGCATTCGGTCTTGACCGTCTGACCATGCTGCTGACCGGCACCGACAATATCCGTGACGTTATCGCCTTCCCGAAAACCACGGCGGCAGCGTGTC" +
                  "TGATGACTGAAGCACCGAGCTTTGCTAACCCGACTGCACTGGCTGAGCTGAGCATTCAGGTTGTGAAGAAGGCTGAGAATAACTGA", gene.getSequenceAsString());
  
          // compare translation
          assertEquals("MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDM" +
                  "ATGEIEVLASSLTIINRADVLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKF" +
                  "YALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREVMEALVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLR" +
                  "NPMELTDVADLLKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLAYIKVNERAKGLEGINSPVAKFLNAEIIEDILDRTAAQ" +
                  "DGDMIFFGADNKKIVADAMGALRLKVGKDLGLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTAAELKAAPENAVANAYDMVINGYEVGGGS" +
                  "VRIHNGDMQQTVFGILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPTALAELSIQVVKKA" +
                  "ENN", translation.getSequenceAsString());
  
          // ensure correct UniProt mapping
          assertEquals("P21889", translation.getFeature(UniProtIdentifier.class).getContent());
      }
test_case.class_method_signature: ENAParserServiceTest.shouldParseNucleotideSequence()
test_case.full_signature: @Test void shouldParseNucleotideSequence()
test_case.identifier: shouldParseNucleotideSequence
test_case.invocations: parseGeneTranslationPair getGene getTranslation assertEquals getSequenceAsString assertEquals getSequenceAsString assertEquals getContent getFeature
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldParseNucleotideSequence()
focal_class.declarator: logger = LoggerFactory.getLogger(ENAParserService.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(ENAParserService.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: ENA_FETCH_URL = "https://www.ebi.ac.uk/ena/data/view/%s&display=xml"
focal_class.modifier: private static final
focal_class.original_string: private static final String ENA_FETCH_URL = "https://www.ebi.ac.uk/ena/data/view/%s&display=xml";
focal_class.type: String
focal_class.var_name: ENA_FETCH_URL
focal_class.file: singa-sequence/src/main/java/bio/singa/sequence/parser/ena/ENAParserService.java
focal_class.identifier: ENAParserService
focal_class.class_method_signature: ENAParserService.ENAParserService(ENAAccessionNumber enaAccessionNumber)
focal_class.full_signature: public  ENAParserService(ENAAccessionNumber enaAccessionNumber)
focal_class.identifier: ENAParserService
focal_class.modifiers: public
focal_class.parameters: (ENAAccessionNumber enaAccessionNumber)
focal_class.signature:  ENAParserService(ENAAccessionNumber enaAccessionNumber)
focal_class.class_method_signature: ENAParserService.parse(String enaAccessionNumber)
focal_class.full_signature: public static NucleotideSequence parse(String enaAccessionNumber)
focal_class.identifier: parse
focal_class.modifiers: public static
focal_class.parameters: (String enaAccessionNumber)
focal_class.return: NucleotideSequence
focal_class.signature: NucleotideSequence parse(String enaAccessionNumber)
focal_class.class_method_signature: ENAParserService.parse(ENAAccessionNumber enaAccessionNumber)
focal_class.full_signature: public static NucleotideSequence parse(ENAAccessionNumber enaAccessionNumber)
focal_class.identifier: parse
focal_class.modifiers: public static
focal_class.parameters: (ENAAccessionNumber enaAccessionNumber)
focal_class.return: NucleotideSequence
focal_class.signature: NucleotideSequence parse(ENAAccessionNumber enaAccessionNumber)
focal_class.class_method_signature: ENAParserService.parseGeneTranslationPair(String enaAccessionNumber)
focal_class.full_signature: public static SequenceContainer parseGeneTranslationPair(String enaAccessionNumber)
focal_class.identifier: parseGeneTranslationPair
focal_class.modifiers: public static
focal_class.parameters: (String enaAccessionNumber)
focal_class.return: SequenceContainer
focal_class.signature: SequenceContainer parseGeneTranslationPair(String enaAccessionNumber)
focal_class.class_method_signature: ENAParserService.parseGeneTranslationPair(ENAAccessionNumber enaAccessionNumber)
focal_class.full_signature: public static SequenceContainer parseGeneTranslationPair(ENAAccessionNumber enaAccessionNumber)
focal_class.identifier: parseGeneTranslationPair
focal_class.modifiers: public static
focal_class.parameters: (ENAAccessionNumber enaAccessionNumber)
focal_class.return: SequenceContainer
focal_class.signature: SequenceContainer parseGeneTranslationPair(ENAAccessionNumber enaAccessionNumber)
focal_class.class_method_signature: ENAParserService.parseXML()
focal_class.full_signature: private void parseXML()
focal_class.identifier: parseXML
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parseXML()
focal_class.class_method_signature: ENAParserService.parse()
focal_class.full_signature: @Override public NucleotideSequence parse()
focal_class.identifier: parse
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: NucleotideSequence
focal_class.signature: NucleotideSequence parse()
focal_class.superclass: extends AbstractXMLParser<NucleotideSequence>
focal_method.body: public static SequenceContainer parseGeneTranslationPair(String enaAccessionNumber) {
          return parseGeneTranslationPair(new ENAAccessionNumber(enaAccessionNumber));
      }
focal_method.class_method_signature: ENAParserService.parseGeneTranslationPair(String enaAccessionNumber)
focal_method.full_signature: public static SequenceContainer parseGeneTranslationPair(String enaAccessionNumber)
focal_method.identifier: parseGeneTranslationPair
focal_method.invocations: parseGeneTranslationPair
focal_method.modifiers: public static
focal_method.parameters: (String enaAccessionNumber)
focal_method.return: SequenceContainer
focal_method.signature: SequenceContainer parseGeneTranslationPair(String enaAccessionNumber)