test_class.declarator: v2sf=null
test_class.modifier: private static
test_class.original_string: private static HpoAnnotationModel v2sf=null;
test_class.type: HpoAnnotationModel
test_class.var_name: v2sf
test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/hpo/HpoAnnotationModelTest.java
test_class.identifier: HpoAnnotationModelTest
test_case.body: @Test
      void basenameTest() {
          Assertions.assertEquals("OMIM-123456.tab", v2sf.getBasename());
      }
test_case.class_method_signature: HpoAnnotationModelTest.basenameTest()
test_case.full_signature: @Test void basenameTest()
test_case.identifier: basenameTest
test_case.invocations: assertEquals getBasename
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void basenameTest()
focal_class.declarator: basename
focal_class.modifier: private final
focal_class.original_string: private final String basename;
focal_class.type: String
focal_class.var_name: basename
focal_class.declarator: entryList
focal_class.modifier: private
focal_class.original_string: private List<HpoAnnotationEntry> entryList;
focal_class.type: List<HpoAnnotationEntry>
focal_class.var_name: entryList
focal_class.declarator: database
focal_class.modifier: private final
focal_class.original_string: private final Database database;
focal_class.type: Database
focal_class.var_name: database
focal_class.declarator: EMPTY_STRING = ""
focal_class.modifier: private static final
focal_class.original_string: private static final String EMPTY_STRING = "";
focal_class.type: String
focal_class.var_name: EMPTY_STRING
focal_class.declarator: n_of_m_pattern = Pattern.compile("^(\\d+)/(\\d+?)")
focal_class.modifier: private final static
focal_class.original_string: private final static Pattern n_of_m_pattern = Pattern.compile("^(\\d+)/(\\d+?)");
focal_class.type: Pattern
focal_class.var_name: n_of_m_pattern
focal_class.declarator: percentage_pattern = Pattern.compile("^(\\d*\\.?\\d+)%")
focal_class.modifier: private final static
focal_class.original_string: private final static Pattern percentage_pattern = Pattern.compile("^(\\d*\\.?\\d+)%");
focal_class.type: Pattern
focal_class.var_name: percentage_pattern
focal_class.declarator: hpoTerm_pattern = Pattern.compile("^HP:\\d{7}$")
focal_class.modifier: private final static
focal_class.original_string: private final static Pattern hpoTerm_pattern = Pattern.compile("^HP:\\d{7}$");
focal_class.type: Pattern
focal_class.var_name: hpoTerm_pattern
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/hpo/HpoAnnotationModel.java
focal_class.identifier: HpoAnnotationModel
focal_class.class_method_signature: HpoAnnotationModel.getBasename()
focal_class.full_signature: public String getBasename()
focal_class.identifier: getBasename
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getBasename()
focal_class.class_method_signature: HpoAnnotationModel.HpoAnnotationModel(String name, List<HpoAnnotationEntry> entries)
focal_class.full_signature: public  HpoAnnotationModel(String name, List<HpoAnnotationEntry> entries)
focal_class.identifier: HpoAnnotationModel
focal_class.modifiers: public
focal_class.parameters: (String name, List<HpoAnnotationEntry> entries)
focal_class.signature:  HpoAnnotationModel(String name, List<HpoAnnotationEntry> entries)
focal_class.class_method_signature: HpoAnnotationModel.mergeWithInheritanceAnnotations(Collection<HpoAnnotationEntry> inherit)
focal_class.full_signature: public HpoAnnotationModel mergeWithInheritanceAnnotations(Collection<HpoAnnotationEntry> inherit)
focal_class.identifier: mergeWithInheritanceAnnotations
focal_class.modifiers: public
focal_class.parameters: (Collection<HpoAnnotationEntry> inherit)
focal_class.return: HpoAnnotationModel
focal_class.signature: HpoAnnotationModel mergeWithInheritanceAnnotations(Collection<HpoAnnotationEntry> inherit)
focal_class.class_method_signature: HpoAnnotationModel.HpoAnnotationModel(String base, Database db, List<HpoAnnotationEntry> entries)
focal_class.full_signature: private  HpoAnnotationModel(String base, Database db, List<HpoAnnotationEntry> entries)
focal_class.identifier: HpoAnnotationModel
focal_class.modifiers: private
focal_class.parameters: (String base, Database db, List<HpoAnnotationEntry> entries)
focal_class.signature:  HpoAnnotationModel(String base, Database db, List<HpoAnnotationEntry> entries)
focal_class.class_method_signature: HpoAnnotationModel.isOMIM()
focal_class.full_signature: public boolean isOMIM()
focal_class.identifier: isOMIM
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isOMIM()
focal_class.class_method_signature: HpoAnnotationModel.isDECIPHER()
focal_class.full_signature: public boolean isDECIPHER()
focal_class.identifier: isDECIPHER
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isDECIPHER()
focal_class.class_method_signature: HpoAnnotationModel.getEntryList()
focal_class.full_signature: public List<HpoAnnotationEntry> getEntryList()
focal_class.identifier: getEntryList
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<HpoAnnotationEntry>
focal_class.signature: List<HpoAnnotationEntry> getEntryList()
focal_class.class_method_signature: HpoAnnotationModel.getNumberOfAnnotations()
focal_class.full_signature: public int getNumberOfAnnotations()
focal_class.identifier: getNumberOfAnnotations
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getNumberOfAnnotations()
focal_class.class_method_signature: HpoAnnotationModel.divergentNegation(List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private boolean divergentNegation(List<HpoAnnotationEntry> entrylist)
focal_class.identifier: divergentNegation
focal_class.modifiers: private
focal_class.parameters: (List<HpoAnnotationEntry> entrylist)
focal_class.return: boolean
focal_class.signature: boolean divergentNegation(List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.divergentSex(List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private boolean divergentSex(List<HpoAnnotationEntry> entrylist)
focal_class.identifier: divergentSex
focal_class.modifiers: private
focal_class.parameters: (List<HpoAnnotationEntry> entrylist)
focal_class.return: boolean
focal_class.signature: boolean divergentSex(List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.divergentOnset(List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private boolean divergentOnset(List<HpoAnnotationEntry> entrylist)
focal_class.identifier: divergentOnset
focal_class.modifiers: private
focal_class.parameters: (List<HpoAnnotationEntry> entrylist)
focal_class.return: boolean
focal_class.signature: boolean divergentOnset(List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergeFrequencies(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String mergeFrequencies(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergeFrequencies
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String mergeFrequencies(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergeModifiers(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String mergeModifiers(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergeModifiers
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String mergeModifiers(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergeDescriptions(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String mergeDescriptions(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergeDescriptions
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String mergeDescriptions(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergePublications(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String mergePublications(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergePublications
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String mergePublications(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.getHighestEvidenceCode(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String getHighestEvidenceCode(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: getHighestEvidenceCode
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String getHighestEvidenceCode(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergeBiocuration(final List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private String mergeBiocuration(final List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergeBiocuration
focal_class.modifiers: private
focal_class.parameters: (final List<HpoAnnotationEntry> entrylist)
focal_class.return: String
focal_class.signature: String mergeBiocuration(final List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.mergeEntries(List<HpoAnnotationEntry> entrylist)
focal_class.full_signature: private HpoAnnotationEntry mergeEntries(List<HpoAnnotationEntry> entrylist)
focal_class.identifier: mergeEntries
focal_class.modifiers: private
focal_class.parameters: (List<HpoAnnotationEntry> entrylist)
focal_class.return: HpoAnnotationEntry
focal_class.signature: HpoAnnotationEntry mergeEntries(List<HpoAnnotationEntry> entrylist)
focal_class.class_method_signature: HpoAnnotationModel.getMergedModel()
focal_class.full_signature: public HpoAnnotationModel getMergedModel()
focal_class.identifier: getMergedModel
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: HpoAnnotationModel
focal_class.signature: HpoAnnotationModel getMergedModel()
focal_class.class_method_signature: HpoAnnotationModel.getDiseaseId()
focal_class.full_signature: public TermId getDiseaseId()
focal_class.identifier: getDiseaseId
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: TermId
focal_class.signature: TermId getDiseaseId()
focal_class.class_method_signature: HpoAnnotationModel.getDiseaseName()
focal_class.full_signature: public String getDiseaseName()
focal_class.identifier: getDiseaseName
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDiseaseName()
focal_class.class_method_signature: HpoAnnotationModel.addInheritanceEntryCollection(Collection<HpoAnnotationEntry> entries)
focal_class.full_signature: public void addInheritanceEntryCollection(Collection<HpoAnnotationEntry> entries)
focal_class.identifier: addInheritanceEntryCollection
focal_class.modifiers: public
focal_class.parameters: (Collection<HpoAnnotationEntry> entries)
focal_class.return: void
focal_class.signature: void addInheritanceEntryCollection(Collection<HpoAnnotationEntry> entries)
focal_method.body: public String getBasename() {
      return basename;
    }
focal_method.class_method_signature: HpoAnnotationModel.getBasename()
focal_method.full_signature: public String getBasename()
focal_method.identifier: getBasename
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: String
focal_method.signature: String getBasename()