test_class.file: singa-structure/src/test/java/bio/singa/structure/parser/ncbi/RefSeqUniProtMapperTest.java
test_class.identifier: RefSeqUniProtMapperTest
test_case.body: @Test
      void map() {
          List<UniProtIdentifier> uniProtIdentifiers = new RefSeqUniProtMapper(new RefSeqIdentifier("NM_199242.2")).parse();
          assertEquals(1, uniProtIdentifiers.size());
          uniProtIdentifiers = new RefSeqUniProtMapper(new RefSeqIdentifier("NM_001242524.1")).parse();
          assertEquals(2, uniProtIdentifiers.size());
      }
test_case.class_method_signature: RefSeqUniProtMapperTest.map()
test_case.full_signature: @Test void map()
test_case.identifier: map
test_case.invocations: parse assertEquals size parse assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void map()
focal_class.declarator: logger = LoggerFactory.getLogger(RefSeqUniProtMapper.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(RefSeqUniProtMapper.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: MAP_URL = "https://www.uniprot.org/uploadlists/?"
focal_class.modifier: private static final
focal_class.original_string: private static final String MAP_URL = "https://www.uniprot.org/uploadlists/?";
focal_class.type: String
focal_class.var_name: MAP_URL
focal_class.declarator: refSeqIdentifier
focal_class.modifier: private
focal_class.original_string: private RefSeqIdentifier refSeqIdentifier;
focal_class.type: RefSeqIdentifier
focal_class.var_name: refSeqIdentifier
focal_class.file: singa-structure/src/main/java/bio/singa/structure/parser/ncbi/RefSeqUniProtMapper.java
focal_class.identifier: RefSeqUniProtMapper
focal_class.class_method_signature: RefSeqUniProtMapper.RefSeqUniProtMapper(RefSeqIdentifier refSeqIdentifier)
focal_class.full_signature: public  RefSeqUniProtMapper(RefSeqIdentifier refSeqIdentifier)
focal_class.identifier: RefSeqUniProtMapper
focal_class.modifiers: public
focal_class.parameters: (RefSeqIdentifier refSeqIdentifier)
focal_class.signature:  RefSeqUniProtMapper(RefSeqIdentifier refSeqIdentifier)
focal_class.class_method_signature: RefSeqUniProtMapper.parse()
focal_class.full_signature: @Override public List<UniProtIdentifier> parse()
focal_class.identifier: parse
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<UniProtIdentifier>
focal_class.signature: List<UniProtIdentifier> parse()
focal_class.superclass: extends AbstractUniProtIdentifierMappingParser<List<UniProtIdentifier>>
focal_method.body: @Override
      public List<UniProtIdentifier> parse() {
          List<UniProtIdentifier> uniProtIdentifiers = new ArrayList<>();
          try {
              BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(getFetchResult()));
              // skip header line
              bufferedReader.readLine();
              String line;
              while ((line = bufferedReader.readLine()) != null) {
                  String[] split = line.split("\t");
                  try {
                      uniProtIdentifiers.add(new UniProtIdentifier(split[0]));
                  } catch (IllegalArgumentException e) {
                      logger.debug("skipping malformed UniProt identifier {}", line);
                  }
              }
          } catch (IOException e) {
              throw new UncheckedIOException("failed to retrieve mapping for " + refSeqIdentifier, e);
          }
          return uniProtIdentifiers;
      }
focal_method.class_method_signature: RefSeqUniProtMapper.parse()
focal_method.full_signature: @Override public List<UniProtIdentifier> parse()
focal_method.identifier: parse
focal_method.invocations: getFetchResult readLine readLine split add debug
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: List<UniProtIdentifier>
focal_method.signature: List<UniProtIdentifier> parse()