test_class.declarator: ontology
test_class.modifier: private static
test_class.original_string: private static Ontology ontology;
test_class.type: Ontology
test_class.var_name: ontology
test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/hpo/HpoAnnotationEntryTest.java
test_class.identifier: HpoAnnotationEntryTest
test_case.body: @Test
      void testEvidenceCodeValid() {
          String[] fields={
                  "OMIM:123456",
                  "MADE-UP SYNDROME",
                  "HP:0000528",
                  "Anophthalmia",
                  "",
                  "",
                  "76.3%",
                  "FEMALE",
                  "",
                  "",
                  "",
                  "PMID:9843983",
                  "PC",
                  "HPO:probinson[2013-01-09]"};
          String line = String.join("\t",fields);//Arrays.stream(fields).collect(Collectors.joining("\t"));
          Assertions.assertThrows(PhenolException.class, () -> {
              HpoAnnotationEntry entry = HpoAnnotationEntry.fromLine(line,ontology);
          });
      }
test_case.class_method_signature: HpoAnnotationEntryTest.testEvidenceCodeValid()
test_case.full_signature: @Test void testEvidenceCodeValid()
test_case.identifier: testEvidenceCodeValid
test_case.invocations: join assertThrows fromLine
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testEvidenceCodeValid()
focal_class.declarator: logger = LoggerFactory.getLogger(HpoAnnotationEntry.class)
focal_class.modifier: private final static
focal_class.original_string: private final static Logger logger = LoggerFactory.getLogger(HpoAnnotationEntry.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: phenotypeRoot = TermId.of("HP:0000118")
focal_class.modifier: private static final
focal_class.original_string: private static final TermId phenotypeRoot = TermId.of("HP:0000118");
focal_class.type: TermId
focal_class.var_name: phenotypeRoot
focal_class.declarator: INHERITANCE_TERM_ID = TermId.of("HP:0000005")
focal_class.modifier: private static final
focal_class.original_string: private static final TermId INHERITANCE_TERM_ID = TermId.of("HP:0000005");
focal_class.type: TermId
focal_class.var_name: INHERITANCE_TERM_ID
focal_class.declarator: CLINICAL_COURSE_ID = TermId.of("HP:0031797")
focal_class.modifier: private static final
focal_class.original_string: private static final TermId CLINICAL_COURSE_ID = TermId.of("HP:0031797");
focal_class.type: TermId
focal_class.var_name: CLINICAL_COURSE_ID
focal_class.declarator: CLINICAL_MODIFIER_ID = TermId.of("HP:0012823")
focal_class.modifier: private static final
focal_class.original_string: private static final TermId CLINICAL_MODIFIER_ID = TermId.of("HP:0012823");
focal_class.type: TermId
focal_class.var_name: CLINICAL_MODIFIER_ID
focal_class.declarator: EMPTY_STRING=""
focal_class.modifier: private final static
focal_class.original_string: private final static String EMPTY_STRING="";
focal_class.type: String
focal_class.var_name: EMPTY_STRING
focal_class.declarator: diseaseID
focal_class.modifier: private final
focal_class.original_string: private final String diseaseID;
focal_class.type: String
focal_class.var_name: diseaseID
focal_class.declarator: diseaseName
focal_class.modifier: private final
focal_class.original_string: private final String diseaseName;
focal_class.type: String
focal_class.var_name: diseaseName
focal_class.declarator: phenotypeId
focal_class.modifier: private final
focal_class.original_string: private final TermId phenotypeId;
focal_class.type: TermId
focal_class.var_name: phenotypeId
focal_class.declarator: phenotypeName
focal_class.modifier: private final
focal_class.original_string: private final String phenotypeName;
focal_class.type: String
focal_class.var_name: phenotypeName
focal_class.declarator: ageOfOnsetId
focal_class.modifier: private final
focal_class.original_string: private final String ageOfOnsetId;
focal_class.type: String
focal_class.var_name: ageOfOnsetId
focal_class.declarator: ageOfOnsetName
focal_class.modifier: private final
focal_class.original_string: private final String ageOfOnsetName;
focal_class.type: String
focal_class.var_name: ageOfOnsetName
focal_class.declarator: evidenceCode
focal_class.modifier: private final
focal_class.original_string: private final String evidenceCode;
focal_class.type: String
focal_class.var_name: evidenceCode
focal_class.declarator: frequencyModifier
focal_class.modifier: private final
focal_class.original_string: private final String frequencyModifier;
focal_class.type: String
focal_class.var_name: frequencyModifier
focal_class.declarator: sex
focal_class.modifier: private final
focal_class.original_string: private final String sex;
focal_class.type: String
focal_class.var_name: sex
focal_class.declarator: negation
focal_class.modifier: private final
focal_class.original_string: private final String negation;
focal_class.type: String
focal_class.var_name: negation
focal_class.declarator: modifier
focal_class.modifier: private final
focal_class.original_string: private final String modifier;
focal_class.type: String
focal_class.var_name: modifier
focal_class.declarator: description
focal_class.modifier: private final
focal_class.original_string: private final String description;
focal_class.type: String
focal_class.var_name: description
focal_class.declarator: publication
focal_class.modifier: private final
focal_class.original_string: private final String publication;
focal_class.type: String
focal_class.var_name: publication
focal_class.declarator: biocuration
focal_class.modifier: private final
focal_class.original_string: private final String biocuration;
focal_class.type: String
focal_class.var_name: biocuration
focal_class.declarator: expectedFields ={"#diseaseID",
              "diseaseName",
              "phenotypeID",
              "phenotypeName",
              "onsetID",
              "onsetName",
              "frequency",
              "sex",
              "negation",
              "modifier",
              "description",
              "publication",
              "evidence",
              "biocuration"}
focal_class.modifier: private final static
focal_class.original_string: private final static String [] expectedFields ={"#diseaseID",
              "diseaseName",
              "phenotypeID",
              "phenotypeName",
              "onsetID",
              "onsetName",
              "frequency",
              "sex",
              "negation",
              "modifier",
              "description",
              "publication",
              "evidence",
              "biocuration"};
focal_class.type: String []
focal_class.var_name: expectedFields
focal_class.declarator: NUMBER_OF_FIELDS=expectedFields.length
focal_class.modifier: private static final
focal_class.original_string: private static final int NUMBER_OF_FIELDS=expectedFields.length;
focal_class.type: int
focal_class.var_name: NUMBER_OF_FIELDS
focal_class.declarator: validDatabases = ImmutableSet.of("OMIM","DECIPHER","ORPHA")
focal_class.modifier: private final static
focal_class.original_string: private final static Set<String> validDatabases = ImmutableSet.of("OMIM","DECIPHER","ORPHA");
focal_class.type: Set<String>
focal_class.var_name: validDatabases
focal_class.declarator: frequencySubhierarcyTermIds = ImmutableSet.of(TermId.of("HP:0003674"),TermId.of("HP:0040280"),
              TermId.of("HP:0040281"), TermId.of("HP:0040282"),TermId.of("HP:0040283"),TermId.of("HP:0040284"),
              TermId.of("HP:0040285"))
focal_class.modifier: private final static
focal_class.original_string: private final static Set<TermId> frequencySubhierarcyTermIds = ImmutableSet.of(TermId.of("HP:0003674"),TermId.of("HP:0040280"),
              TermId.of("HP:0040281"), TermId.of("HP:0040282"),TermId.of("HP:0040283"),TermId.of("HP:0040284"),
              TermId.of("HP:0040285"));
focal_class.type: Set<TermId>
focal_class.var_name: frequencySubhierarcyTermIds
focal_class.declarator: onsetSubhierarcyTermIds = ImmutableSet.of( TermId.of("HP:0003674"), TermId.of("HP:0011460"),
              TermId.of("HP:0003581"), TermId.of("HP:0003596"), TermId.of("HP:0003584"), TermId.of("HP:0011462"),
               TermId.of("HP:0003577"), TermId.of("HP:0003623"), TermId.of("HP:0410280"), TermId.of("HP:0011463"),
               TermId.of("HP:0003593"), TermId.of("HP:0003621"), TermId.of("HP:0030674"), TermId.of("HP:0011461"))
focal_class.modifier: private final static
focal_class.original_string: private final static Set<TermId> onsetSubhierarcyTermIds = ImmutableSet.of( TermId.of("HP:0003674"), TermId.of("HP:0011460"),
              TermId.of("HP:0003581"), TermId.of("HP:0003596"), TermId.of("HP:0003584"), TermId.of("HP:0011462"),
               TermId.of("HP:0003577"), TermId.of("HP:0003623"), TermId.of("HP:0410280"), TermId.of("HP:0011463"),
               TermId.of("HP:0003593"), TermId.of("HP:0003621"), TermId.of("HP:0030674"), TermId.of("HP:0011461"));
focal_class.type: Set<TermId>
focal_class.var_name: onsetSubhierarcyTermIds
focal_class.declarator: EVIDENCE_CODES = ImmutableSet.of("IEA","TAS","PCS")
focal_class.modifier: private static final
focal_class.original_string: private static final Set<String> EVIDENCE_CODES = ImmutableSet.of("IEA","TAS","PCS");
focal_class.type: Set<String>
focal_class.var_name: EVIDENCE_CODES
focal_class.declarator: VALID_CITATION_PREFIXES = ImmutableSet.of("PMID","OMIM","http","https","DECIPHER",
             "ORPHA", "ISBN", "ISBN-10","ISBN-13")
focal_class.modifier: private static final
focal_class.original_string: private static final Set<String> VALID_CITATION_PREFIXES = ImmutableSet.of("PMID","OMIM","http","https","DECIPHER",
             "ORPHA", "ISBN", "ISBN-10","ISBN-13");
focal_class.type: Set<String>
focal_class.var_name: VALID_CITATION_PREFIXES
focal_class.declarator: biocurationRegex = "(\\w+:\\w+)\\[(\\d{4}-\\d{2}-\\d{2})]"
focal_class.modifier: private static final
focal_class.original_string: private static final String biocurationRegex = "(\\w+:\\w+)\\[(\\d{4}-\\d{2}-\\d{2})]";
focal_class.type: String
focal_class.var_name: biocurationRegex
focal_class.declarator: biocurationPattern = Pattern.compile(biocurationRegex)
focal_class.modifier: private static final
focal_class.original_string: private static final Pattern biocurationPattern = Pattern.compile(biocurationRegex);
focal_class.type: Pattern
focal_class.var_name: biocurationPattern
focal_class.declarator: EXCLUDED = TermId.of("HP:0040285")
focal_class.modifier: private static final
focal_class.original_string: private static final TermId EXCLUDED = TermId.of("HP:0040285");
focal_class.type: TermId
focal_class.var_name: EXCLUDED
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/hpo/HpoAnnotationEntry.java
focal_class.identifier: HpoAnnotationEntry
focal_class.class_method_signature: HpoAnnotationEntry.getDiseaseID()
focal_class.full_signature: public String getDiseaseID()
focal_class.identifier: getDiseaseID
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDiseaseID()
focal_class.class_method_signature: HpoAnnotationEntry.getDB()
focal_class.full_signature: public String getDB()
focal_class.identifier: getDB
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDB()
focal_class.class_method_signature: HpoAnnotationEntry.getDB_Object_ID()
focal_class.full_signature: public String getDB_Object_ID()
focal_class.identifier: getDB_Object_ID
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDB_Object_ID()
focal_class.class_method_signature: HpoAnnotationEntry.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: HpoAnnotationEntry.getPhenotypeId()
focal_class.full_signature: public TermId getPhenotypeId()
focal_class.identifier: getPhenotypeId
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: TermId
focal_class.signature: TermId getPhenotypeId()
focal_class.class_method_signature: HpoAnnotationEntry.getPhenotypeLabel()
focal_class.full_signature: public String getPhenotypeLabel()
focal_class.identifier: getPhenotypeLabel
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getPhenotypeLabel()
focal_class.class_method_signature: HpoAnnotationEntry.getAgeOfOnsetId()
focal_class.full_signature: public String getAgeOfOnsetId()
focal_class.identifier: getAgeOfOnsetId
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAgeOfOnsetId()
focal_class.class_method_signature: HpoAnnotationEntry.getAgeOfOnsetLabel()
focal_class.full_signature: public String getAgeOfOnsetLabel()
focal_class.identifier: getAgeOfOnsetLabel
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAgeOfOnsetLabel()
focal_class.class_method_signature: HpoAnnotationEntry.getEvidenceCode()
focal_class.full_signature: public String getEvidenceCode()
focal_class.identifier: getEvidenceCode
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getEvidenceCode()
focal_class.class_method_signature: HpoAnnotationEntry.getFrequencyModifier()
focal_class.full_signature: public String getFrequencyModifier()
focal_class.identifier: getFrequencyModifier
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getFrequencyModifier()
focal_class.class_method_signature: HpoAnnotationEntry.getSex()
focal_class.full_signature: public String getSex()
focal_class.identifier: getSex
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getSex()
focal_class.class_method_signature: HpoAnnotationEntry.getNegation()
focal_class.full_signature: public String getNegation()
focal_class.identifier: getNegation
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getNegation()
focal_class.class_method_signature: HpoAnnotationEntry.getModifier()
focal_class.full_signature: public String getModifier()
focal_class.identifier: getModifier
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getModifier()
focal_class.class_method_signature: HpoAnnotationEntry.getDescription()
focal_class.full_signature: public String getDescription()
focal_class.identifier: getDescription
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDescription()
focal_class.class_method_signature: HpoAnnotationEntry.getPublication()
focal_class.full_signature: public String getPublication()
focal_class.identifier: getPublication
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getPublication()
focal_class.class_method_signature: HpoAnnotationEntry.getBiocuration()
focal_class.full_signature: public String getBiocuration()
focal_class.identifier: getBiocuration
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getBiocuration()
focal_class.class_method_signature: HpoAnnotationEntry.HpoAnnotationEntry(String disID,
                                 String diseaseName,
                                 TermId phenotypeId,
                                 String phenotypeName,
                                 String ageOfOnsetId,
                                 String ageOfOnsetName,
                                 String frequencyString,
                                 String sex,
                                 String negation,
                                 String modifier,
                                 String description,
                                 String publication,
                                 String evidenceCode,
                                 String biocuration)
focal_class.full_signature:   HpoAnnotationEntry(String disID,
                                 String diseaseName,
                                 TermId phenotypeId,
                                 String phenotypeName,
                                 String ageOfOnsetId,
                                 String ageOfOnsetName,
                                 String frequencyString,
                                 String sex,
                                 String negation,
                                 String modifier,
                                 String description,
                                 String publication,
                                 String evidenceCode,
                                 String biocuration)
focal_class.identifier: HpoAnnotationEntry
focal_class.parameters: (String disID,
                                 String diseaseName,
                                 TermId phenotypeId,
                                 String phenotypeName,
                                 String ageOfOnsetId,
                                 String ageOfOnsetName,
                                 String frequencyString,
                                 String sex,
                                 String negation,
                                 String modifier,
                                 String description,
                                 String publication,
                                 String evidenceCode,
                                 String biocuration)
focal_class.signature:  HpoAnnotationEntry(String disID,
                                 String diseaseName,
                                 TermId phenotypeId,
                                 String phenotypeName,
                                 String ageOfOnsetId,
                                 String ageOfOnsetName,
                                 String frequencyString,
                                 String sex,
                                 String negation,
                                 String modifier,
                                 String description,
                                 String publication,
                                 String evidenceCode,
                                 String biocuration)
focal_class.class_method_signature: HpoAnnotationEntry.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.class_method_signature: HpoAnnotationEntry.getLineNoTabs()
focal_class.full_signature: public String getLineNoTabs()
focal_class.identifier: getLineNoTabs
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getLineNoTabs()
focal_class.class_method_signature: HpoAnnotationEntry.getRow()
focal_class.full_signature: public String getRow()
focal_class.identifier: getRow
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getRow()
focal_class.class_method_signature: HpoAnnotationEntry.fromLine(String line, Ontology ontology)
focal_class.full_signature: public static HpoAnnotationEntry fromLine(String line, Ontology ontology)
focal_class.identifier: fromLine
focal_class.modifiers: public static
focal_class.parameters: (String line, Ontology ontology)
focal_class.return: HpoAnnotationEntry
focal_class.signature: HpoAnnotationEntry fromLine(String line, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.fromLineReplaceObsoletePhenotypeData(String line, Ontology ontology)
focal_class.full_signature: public static Optional<HpoAnnotationEntry> fromLineReplaceObsoletePhenotypeData(String line, Ontology ontology)
focal_class.identifier: fromLineReplaceObsoletePhenotypeData
focal_class.modifiers: public static
focal_class.parameters: (String line, Ontology ontology)
focal_class.return: Optional<HpoAnnotationEntry>
focal_class.signature: Optional<HpoAnnotationEntry> fromLineReplaceObsoletePhenotypeData(String line, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.fromOrphaData(String diseaseID,
                                                     String diseaseName,
                                                     String hpoId,
                                                     String hpoLabel,
                                                     TermId frequency,
                                                     Ontology ontology,
                                                     String biocuration,
                                                     boolean replaceObsoleteTermId)
focal_class.full_signature: public static HpoAnnotationEntry fromOrphaData(String diseaseID,
                                                     String diseaseName,
                                                     String hpoId,
                                                     String hpoLabel,
                                                     TermId frequency,
                                                     Ontology ontology,
                                                     String biocuration,
                                                     boolean replaceObsoleteTermId)
focal_class.identifier: fromOrphaData
focal_class.modifiers: public static
focal_class.parameters: (String diseaseID,
                                                     String diseaseName,
                                                     String hpoId,
                                                     String hpoLabel,
                                                     TermId frequency,
                                                     Ontology ontology,
                                                     String biocuration,
                                                     boolean replaceObsoleteTermId)
focal_class.return: HpoAnnotationEntry
focal_class.signature: HpoAnnotationEntry fromOrphaData(String diseaseID,
                                                     String diseaseName,
                                                     String hpoId,
                                                     String hpoLabel,
                                                     TermId frequency,
                                                     Ontology ontology,
                                                     String biocuration,
                                                     boolean replaceObsoleteTermId)
focal_class.class_method_signature: HpoAnnotationEntry.fromOrphaInheritanceData(String diseaseID,
                                                   String diseaseName,
                                                   TermId hpoInheritanceId,
                                                   String hpoLabel,
                                                   String biocuration)
focal_class.full_signature: public static HpoAnnotationEntry fromOrphaInheritanceData(String diseaseID,
                                                   String diseaseName,
                                                   TermId hpoInheritanceId,
                                                   String hpoLabel,
                                                   String biocuration)
focal_class.identifier: fromOrphaInheritanceData
focal_class.modifiers: public static
focal_class.parameters: (String diseaseID,
                                                   String diseaseName,
                                                   TermId hpoInheritanceId,
                                                   String hpoLabel,
                                                   String biocuration)
focal_class.return: HpoAnnotationEntry
focal_class.signature: HpoAnnotationEntry fromOrphaInheritanceData(String diseaseID,
                                                   String diseaseName,
                                                   TermId hpoInheritanceId,
                                                   String hpoLabel,
                                                   String biocuration)
focal_class.class_method_signature: HpoAnnotationEntry.performQualityControl(HpoAnnotationEntry entry, Ontology ontology)
focal_class.full_signature: private static void performQualityControl(HpoAnnotationEntry entry, Ontology ontology)
focal_class.identifier: performQualityControl
focal_class.modifiers: private static
focal_class.parameters: (HpoAnnotationEntry entry, Ontology ontology)
focal_class.return: void
focal_class.signature: void performQualityControl(HpoAnnotationEntry entry, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.checkDB(HpoAnnotationEntry entry)
focal_class.full_signature: private static void checkDB(HpoAnnotationEntry entry)
focal_class.identifier: checkDB
focal_class.modifiers: private static
focal_class.parameters: (HpoAnnotationEntry entry)
focal_class.return: void
focal_class.signature: void checkDB(HpoAnnotationEntry entry)
focal_class.class_method_signature: HpoAnnotationEntry.checkDiseaseName(String name)
focal_class.full_signature: private static void checkDiseaseName(String name)
focal_class.identifier: checkDiseaseName
focal_class.modifiers: private static
focal_class.parameters: (String name)
focal_class.return: void
focal_class.signature: void checkDiseaseName(String name)
focal_class.class_method_signature: HpoAnnotationEntry.checkPhenotypeFields(HpoAnnotationEntry entry, Ontology ontology)
focal_class.full_signature: private static void checkPhenotypeFields(HpoAnnotationEntry entry, Ontology ontology)
focal_class.identifier: checkPhenotypeFields
focal_class.modifiers: private static
focal_class.parameters: (HpoAnnotationEntry entry, Ontology ontology)
focal_class.return: void
focal_class.signature: void checkPhenotypeFields(HpoAnnotationEntry entry, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.checkAgeOfOnsetFields(String id, String termLabel, Ontology ontology)
focal_class.full_signature: private static void checkAgeOfOnsetFields(String id, String termLabel, Ontology ontology)
focal_class.identifier: checkAgeOfOnsetFields
focal_class.modifiers: private static
focal_class.parameters: (String id, String termLabel, Ontology ontology)
focal_class.return: void
focal_class.signature: void checkAgeOfOnsetFields(String id, String termLabel, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.checkEvidence(String evi)
focal_class.full_signature: private static void checkEvidence(String evi)
focal_class.identifier: checkEvidence
focal_class.modifiers: private static
focal_class.parameters: (String evi)
focal_class.return: void
focal_class.signature: void checkEvidence(String evi)
focal_class.class_method_signature: HpoAnnotationEntry.checkFrequency(String freq, Ontology ontology)
focal_class.full_signature: private static void checkFrequency(String freq, Ontology ontology)
focal_class.identifier: checkFrequency
focal_class.modifiers: private static
focal_class.parameters: (String freq, Ontology ontology)
focal_class.return: void
focal_class.signature: void checkFrequency(String freq, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.checkSexEntry(String sex)
focal_class.full_signature: private static void checkSexEntry(String sex)
focal_class.identifier: checkSexEntry
focal_class.modifiers: private static
focal_class.parameters: (String sex)
focal_class.return: void
focal_class.signature: void checkSexEntry(String sex)
focal_class.class_method_signature: HpoAnnotationEntry.checkNegation(String negation)
focal_class.full_signature: private static void checkNegation(String negation)
focal_class.identifier: checkNegation
focal_class.modifiers: private static
focal_class.parameters: (String negation)
focal_class.return: void
focal_class.signature: void checkNegation(String negation)
focal_class.class_method_signature: HpoAnnotationEntry.checkModifier(String modifierString, Ontology ontology)
focal_class.full_signature: private static void checkModifier(String modifierString, Ontology ontology)
focal_class.identifier: checkModifier
focal_class.modifiers: private static
focal_class.parameters: (String modifierString, Ontology ontology)
focal_class.return: void
focal_class.signature: void checkModifier(String modifierString, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.checkPublication(String pub)
focal_class.full_signature: private static void checkPublication(String pub)
focal_class.identifier: checkPublication
focal_class.modifiers: private static
focal_class.parameters: (String pub)
focal_class.return: void
focal_class.signature: void checkPublication(String pub)
focal_class.class_method_signature: HpoAnnotationEntry.checkBiocuration(String entrylist)
focal_class.full_signature: private static void checkBiocuration(String entrylist)
focal_class.identifier: checkBiocuration
focal_class.modifiers: private static
focal_class.parameters: (String entrylist)
focal_class.return: void
focal_class.signature: void checkBiocuration(String entrylist)
focal_class.class_method_signature: HpoAnnotationEntry.getAspect(TermId tid, Ontology ontology)
focal_class.full_signature: private String getAspect(TermId tid, Ontology ontology)
focal_class.identifier: getAspect
focal_class.modifiers: private
focal_class.parameters: (TermId tid, Ontology ontology)
focal_class.return: String
focal_class.signature: String getAspect(TermId tid, Ontology ontology)
focal_class.class_method_signature: HpoAnnotationEntry.toBigFileLine(Ontology ontology)
focal_class.full_signature: public String toBigFileLine(Ontology ontology)
focal_class.identifier: toBigFileLine
focal_class.modifiers: public
focal_class.parameters: (Ontology ontology)
focal_class.return: String
focal_class.signature: String toBigFileLine(Ontology ontology)
focal_method.body: public static HpoAnnotationEntry fromLine(String line, Ontology ontology) throws PhenolException {
          String [] A= line.split("\t");
          if (A.length!= NUMBER_OF_FIELDS) {
              throw new HpoAnnotationModelException(String.format("We were expecting %d expectedFields but got %d for line %s",NUMBER_OF_FIELDS,A.length,line ));
          }
          String diseaseID=A[0];
          String diseaseName=A[1];
          TermId phenotypeId = TermId.of(A[2]);
          String phenotypeName=A[3];
          String ageOfOnsetId=A[4];
          String ageOfOnsetName=A[5];
          String frequencyString=A[6];
          String sex=A[7];
          String negation=A[8];
          String modifier=A[9];
          String description=A[10];
          String publication=A[11];
          String evidenceCode=A[12];
          String biocuration=A[13];
  
          HpoAnnotationEntry entry = new HpoAnnotationEntry(diseaseID,
                   diseaseName,
                   phenotypeId,
                   phenotypeName,
                   ageOfOnsetId,
                   ageOfOnsetName,
                   frequencyString,
                   sex,
                   negation,
                   modifier,
                   description,
                   publication,
                   evidenceCode,
                   biocuration);
          // if the following method does not throw an Exception, we are good to go!
          performQualityControl(entry, ontology);
          return entry;
      }
focal_method.class_method_signature: HpoAnnotationEntry.fromLine(String line, Ontology ontology)
focal_method.full_signature: public static HpoAnnotationEntry fromLine(String line, Ontology ontology)
focal_method.identifier: fromLine
focal_method.invocations: split format of performQualityControl
focal_method.modifiers: public static
focal_method.parameters: (String line, Ontology ontology)
focal_method.return: HpoAnnotationEntry
focal_method.signature: HpoAnnotationEntry fromLine(String line, Ontology ontology)