test_class.file: singa-structure/src/test/java/bio/singa/structure/parser/pfam/PfamParserTest.java
test_class.identifier: PfamParserTest
test_case.body: @Test
      void shouldParseChains() {
          List<Chain> chains = PfamParser.create()
                  .version(PfamParser.PfamVersion.V31)
                  .pfamIdentifier("PF17480")
                  .all()
                  .chains();
          assertEquals(2, chains.size());
      }
test_case.class_method_signature: PfamParserTest.shouldParseChains()
test_case.full_signature: @Test void shouldParseChains()
test_case.identifier: shouldParseChains
test_case.invocations: chains all pfamIdentifier version create assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldParseChains()
focal_class.declarator: DEFAULT_CHAIN_LIST_SEPARATOR = "\t"
focal_class.modifier: private static final
focal_class.original_string: private static final String DEFAULT_CHAIN_LIST_SEPARATOR = "\t";
focal_class.type: String
focal_class.var_name: DEFAULT_CHAIN_LIST_SEPARATOR
focal_class.declarator: LEAF_SUBSTRUCTURE_FILTER = leafSubstructure -> !(leafSubstructure instanceof AminoAcid)
focal_class.modifier: private static final
focal_class.original_string: private static final Predicate<LeafSubstructure<?>> LEAF_SUBSTRUCTURE_FILTER = leafSubstructure -> !(leafSubstructure instanceof AminoAcid);
focal_class.type: Predicate<LeafSubstructure<?>>
focal_class.var_name: LEAF_SUBSTRUCTURE_FILTER
focal_class.declarator: logger = LoggerFactory.getLogger(PfamParser.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(PfamParser.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: version
focal_class.modifier: private final
focal_class.original_string: private final PfamVersion version;
focal_class.type: PfamVersion
focal_class.var_name: version
focal_class.declarator: pfamIdentifier
focal_class.modifier: private final
focal_class.original_string: private final PfamIdentifier pfamIdentifier;
focal_class.type: PfamIdentifier
focal_class.var_name: pfamIdentifier
focal_class.declarator: chainListPath
focal_class.modifier: private final
focal_class.original_string: private final Path chainListPath;
focal_class.type: Path
focal_class.var_name: chainListPath
focal_class.declarator: chainListSeparator
focal_class.modifier: private final
focal_class.original_string: private final String chainListSeparator;
focal_class.type: String
focal_class.var_name: chainListSeparator
focal_class.declarator: parseChains
focal_class.modifier: private final
focal_class.original_string: private final boolean parseChains;
focal_class.type: boolean
focal_class.var_name: parseChains
focal_class.declarator: structureParserOptions
focal_class.modifier: private final
focal_class.original_string: private final StructureParserOptions structureParserOptions;
focal_class.type: StructureParserOptions
focal_class.var_name: structureParserOptions
focal_class.declarator: domains
focal_class.modifier: private
focal_class.original_string: private List<List<LeafSubstructure<?>>> domains;
focal_class.type: List<List<LeafSubstructure<?>>>
focal_class.var_name: domains
focal_class.declarator: chains
focal_class.modifier: private
focal_class.original_string: private List<Chain> chains;
focal_class.type: List<Chain>
focal_class.var_name: chains
focal_class.declarator: relevantLines
focal_class.modifier: private
focal_class.original_string: private List<String> relevantLines;
focal_class.type: List<String>
focal_class.var_name: relevantLines
focal_class.file: singa-structure/src/main/java/bio/singa/structure/parser/pfam/PfamParser.java
focal_class.identifier: PfamParser
focal_class.class_method_signature: PfamParser.PfamParser(Builder builder)
focal_class.full_signature: public  PfamParser(Builder builder)
focal_class.identifier: PfamParser
focal_class.modifiers: public
focal_class.parameters: (Builder builder)
focal_class.signature:  PfamParser(Builder builder)
focal_class.class_method_signature: PfamParser.create()
focal_class.full_signature: public static VersionStep create()
focal_class.identifier: create
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: VersionStep
focal_class.signature: VersionStep create()
focal_class.class_method_signature: PfamParser.parse()
focal_class.full_signature: private void parse()
focal_class.identifier: parse
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parse()
focal_class.class_method_signature: PfamParser.parseDomains()
focal_class.full_signature: private void parseDomains()
focal_class.identifier: parseDomains
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parseDomains()
focal_class.class_method_signature: PfamParser.parseChains()
focal_class.full_signature: private void parseChains()
focal_class.identifier: parseChains
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parseChains()
focal_class.class_method_signature: PfamParser.fetchMappingFile()
focal_class.full_signature: private void fetchMappingFile()
focal_class.identifier: fetchMappingFile
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void fetchMappingFile()
focal_class.class_method_signature: PfamParser.getDomains()
focal_class.full_signature: public List<List<LeafSubstructure<?>>> getDomains()
focal_class.identifier: getDomains
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<LeafSubstructure<?>>>
focal_class.signature: List<List<LeafSubstructure<?>>> getDomains()
focal_class.class_method_signature: PfamParser.getChains()
focal_class.full_signature: public List<Chain> getChains()
focal_class.identifier: getChains
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Chain>
focal_class.signature: List<Chain> getChains()
focal_method.body: public static VersionStep create() {
          return new PfamParser.Builder();
      }
focal_method.class_method_signature: PfamParser.create()
focal_method.full_signature: public static VersionStep create()
focal_method.identifier: create
focal_method.modifiers: public static
focal_method.parameters: ()
focal_method.return: VersionStep
focal_method.signature: VersionStep create()