test_class.declarator: genePhenoPath
test_class.modifier: private static
test_class.original_string: private static String genePhenoPath;
test_class.type: String
test_class.var_name: genePhenoPath
test_class.declarator: phenoSexPath
test_class.modifier: private static
test_class.original_string: private static String phenoSexPath;
test_class.type: String
test_class.var_name: phenoSexPath
test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/obo/mpo/MpAnnotationParserTest.java
test_class.identifier: MpAnnotationParserTest
test_case.body: @Test
    void testParseModelMgi5306347() {
      Map<TermId, MpSimpleModel> modelmap = MpAnnotationParser.loadIndividualModels(genePhenoPath);
      TermId kit = TermId.of("MGI:5306347");
      MpSimpleModel model = modelmap.get(kit);
      assertNotNull(model);
      List<MpAnnotation> annots = model.getPhenotypicAbnormalities();
      int expected_number_of_MP_terms=5;
      assertEquals(expected_number_of_MP_terms,annots.size());
      assertFalse(model.hasSexSpecificAnnotation());
    }
test_case.class_method_signature: MpAnnotationParserTest.testParseModelMgi5306347()
test_case.full_signature: @Test void testParseModelMgi5306347()
test_case.identifier: testParseModelMgi5306347
test_case.invocations: loadIndividualModels of get assertNotNull getPhenotypicAbnormalities assertEquals size assertFalse hasSexSpecificAnnotation
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testParseModelMgi5306347()
focal_class.declarator: genePhenoPath
focal_class.modifier: private final
focal_class.original_string: private final String genePhenoPath;
focal_class.type: String
focal_class.var_name: genePhenoPath
focal_class.declarator: phenoSexPath
focal_class.modifier: private final
focal_class.original_string: private final String phenoSexPath;
focal_class.type: String
focal_class.var_name: phenoSexPath
focal_class.declarator: geno2ssannotMap = ImmutableMap.of()
focal_class.modifier: private
focal_class.original_string: private Map<TermId, Map<TermId, MpAnnotation>> geno2ssannotMap = ImmutableMap.of();
focal_class.type: Map<TermId, Map<TermId, MpAnnotation>>
focal_class.var_name: geno2ssannotMap
focal_class.declarator: genotypeAccessionToMpSimpleModelMap
focal_class.modifier: private
focal_class.original_string: private Map<TermId, MpSimpleModel> genotypeAccessionToMpSimpleModelMap;
focal_class.type: Map<TermId, MpSimpleModel>
focal_class.var_name: genotypeAccessionToMpSimpleModelMap
focal_class.declarator: verbose = true
focal_class.modifier: private
focal_class.original_string: private boolean verbose = true;
focal_class.type: boolean
focal_class.var_name: verbose
focal_class.declarator: parseErrors
focal_class.modifier: private final
focal_class.original_string: private final List<String> parseErrors;
focal_class.type: List<String>
focal_class.var_name: parseErrors
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/obo/mpo/MpAnnotationParser.java
focal_class.identifier: MpAnnotationParser
focal_class.class_method_signature: MpAnnotationParser.MpAnnotationParser(String path)
focal_class.full_signature: private  MpAnnotationParser(String path)
focal_class.identifier: MpAnnotationParser
focal_class.modifiers: private
focal_class.parameters: (String path)
focal_class.signature:  MpAnnotationParser(String path)
focal_class.class_method_signature: MpAnnotationParser.MpAnnotationParser(String genePhenoPath, String phenoSexPath)
focal_class.full_signature: private  MpAnnotationParser(String genePhenoPath, String phenoSexPath)
focal_class.identifier: MpAnnotationParser
focal_class.modifiers: private
focal_class.parameters: (String genePhenoPath, String phenoSexPath)
focal_class.signature:  MpAnnotationParser(String genePhenoPath, String phenoSexPath)
focal_class.class_method_signature: MpAnnotationParser.loadIndividualModels(String genePhenoPath)
focal_class.full_signature: public static Map<TermId, MpSimpleModel> loadIndividualModels(String genePhenoPath)
focal_class.identifier: loadIndividualModels
focal_class.modifiers: public static
focal_class.parameters: (String genePhenoPath)
focal_class.return: Map<TermId, MpSimpleModel>
focal_class.signature: Map<TermId, MpSimpleModel> loadIndividualModels(String genePhenoPath)
focal_class.class_method_signature: MpAnnotationParser.loadIndividualModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.full_signature: public static Map<TermId, MpSimpleModel> loadIndividualModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.identifier: loadIndividualModelsWithSexSpecificPhenotypes
focal_class.modifiers: public static
focal_class.parameters: (String genePhenoPath, String phenoSexPath)
focal_class.return: Map<TermId, MpSimpleModel>
focal_class.signature: Map<TermId, MpSimpleModel> loadIndividualModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.class_method_signature: MpAnnotationParser.loadMpGeneModels(String genePhenoPath)
focal_class.full_signature: public static Map<TermId, MpGeneModel> loadMpGeneModels(String genePhenoPath)
focal_class.identifier: loadMpGeneModels
focal_class.modifiers: public static
focal_class.parameters: (String genePhenoPath)
focal_class.return: Map<TermId, MpGeneModel>
focal_class.signature: Map<TermId, MpGeneModel> loadMpGeneModels(String genePhenoPath)
focal_class.class_method_signature: MpAnnotationParser.loadMpGeneModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.full_signature: public static Map<TermId, MpGeneModel> loadMpGeneModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.identifier: loadMpGeneModelsWithSexSpecificPhenotypes
focal_class.modifiers: public static
focal_class.parameters: (String genePhenoPath, String phenoSexPath)
focal_class.return: Map<TermId, MpGeneModel>
focal_class.signature: Map<TermId, MpGeneModel> loadMpGeneModelsWithSexSpecificPhenotypes(String genePhenoPath, String phenoSexPath)
focal_class.class_method_signature: MpAnnotationParser.parsePhenoSexData()
focal_class.full_signature: private void parsePhenoSexData()
focal_class.identifier: parsePhenoSexData
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parsePhenoSexData()
focal_class.class_method_signature: MpAnnotationParser.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_method.body: public static Map<TermId, MpSimpleModel> loadIndividualModels(String genePhenoPath) {
      //Map<TermId, List<MpSimpleModel>> gene2simpleMap = new HashMap<>();
      ImmutableMap.Builder<TermId, MpGeneModel> builder = new ImmutableMap.Builder<>();
      MpAnnotationParser annotParser = new MpAnnotationParser(genePhenoPath);
      if (annotParser.genotypeAccessionToMpSimpleModelMap.isEmpty()) {
        for (String e : annotParser.parseErrors) {
          System.err.println(e);
        }
        throw new PhenolRuntimeException("Could not parse " + genePhenoPath);
      }
      return annotParser.genotypeAccessionToMpSimpleModelMap;
    }
focal_method.class_method_signature: MpAnnotationParser.loadIndividualModels(String genePhenoPath)
focal_method.full_signature: public static Map<TermId, MpSimpleModel> loadIndividualModels(String genePhenoPath)
focal_method.identifier: loadIndividualModels
focal_method.invocations: isEmpty println
focal_method.modifiers: public static
focal_method.parameters: (String genePhenoPath)
focal_method.return: Map<TermId, MpSimpleModel>
focal_method.signature: Map<TermId, MpSimpleModel> loadIndividualModels(String genePhenoPath)