test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/hpo/PhenotypeDotHpoaFileWriterTest.java
test_class.identifier: PhenotypeDotHpoaFileWriterTest
test_case.body: @Test
      void testV2Header() {
          String expected="#DatabaseID\tDiseaseName\tQualifier\tHPO_ID\tReference\tEvidence\tOnset\tFrequency\tSex\tModifier\tAspect\tBiocuration";
          assertEquals(expected,PhenotypeDotHpoaFileWriter.getHeaderLine());
      }
test_case.class_method_signature: PhenotypeDotHpoaFileWriterTest.testV2Header()
test_case.full_signature: @Test void testV2Header()
test_case.identifier: testV2Header
test_case.invocations: assertEquals getHeaderLine
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void testV2Header()
focal_class.declarator: logger = LoggerFactory.getLogger(PhenotypeDotHpoaFileWriter.class)
focal_class.modifier: private final static
focal_class.original_string: private final static Logger logger = LoggerFactory.getLogger(PhenotypeDotHpoaFileWriter.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: internalAnnotationModelList
focal_class.modifier: private final
focal_class.original_string: private final List<HpoAnnotationModel> internalAnnotationModelList;
focal_class.type: List<HpoAnnotationModel>
focal_class.var_name: internalAnnotationModelList
focal_class.declarator: orphanetSmallFileList
focal_class.modifier: private final
focal_class.original_string: private final List<HpoAnnotationModel> orphanetSmallFileList;
focal_class.type: List<HpoAnnotationModel>
focal_class.var_name: orphanetSmallFileList
focal_class.declarator: inheritanceMultiMap
focal_class.modifier: private final
focal_class.original_string: private final Multimap<TermId, HpoAnnotationEntry> inheritanceMultiMap;
focal_class.type: Multimap<TermId, HpoAnnotationEntry>
focal_class.var_name: inheritanceMultiMap
focal_class.declarator: tolerant
focal_class.modifier: private final
focal_class.original_string: private final boolean tolerant;
focal_class.type: boolean
focal_class.var_name: tolerant
focal_class.declarator: merge_frequency
focal_class.modifier: private final
focal_class.original_string: private final boolean merge_frequency;
focal_class.type: boolean
focal_class.var_name: merge_frequency
focal_class.declarator: outputFileName
focal_class.modifier: private final
focal_class.original_string: private final String outputFileName;
focal_class.type: String
focal_class.var_name: outputFileName
focal_class.declarator: ontology
focal_class.modifier: private final
focal_class.original_string: private final Ontology ontology;
focal_class.type: Ontology
focal_class.var_name: ontology
focal_class.declarator: n_orphanet
focal_class.modifier: private
focal_class.original_string: private int n_orphanet;
focal_class.type: int
focal_class.var_name: n_orphanet
focal_class.declarator: n_decipher
focal_class.modifier: private
focal_class.original_string: private int n_decipher;
focal_class.type: int
focal_class.var_name: n_decipher
focal_class.declarator: n_omim
focal_class.modifier: private
focal_class.original_string: private int n_omim;
focal_class.type: int
focal_class.var_name: n_omim
focal_class.declarator: n_unknown
focal_class.modifier: private
focal_class.original_string: private int n_unknown;
focal_class.type: int
focal_class.var_name: n_unknown
focal_class.declarator: ontologyMetaInfo
focal_class.modifier: private
focal_class.original_string: private Map<String, String> ontologyMetaInfo;
focal_class.type: Map<String, String>
focal_class.var_name: ontologyMetaInfo
focal_class.declarator: smallFileDirectory
focal_class.modifier: private final
focal_class.original_string: private final File smallFileDirectory;
focal_class.type: File
focal_class.var_name: smallFileDirectory
focal_class.declarator: orphaPhenotypeXMLfile
focal_class.modifier: private final
focal_class.original_string: private final File orphaPhenotypeXMLfile;
focal_class.type: File
focal_class.var_name: orphaPhenotypeXMLfile
focal_class.declarator: orphaInheritanceXMLfile
focal_class.modifier: private final
focal_class.original_string: private final File orphaInheritanceXMLfile;
focal_class.type: File
focal_class.var_name: orphaInheritanceXMLfile
focal_class.declarator: parseResultAndErrorSummaryLines
focal_class.modifier: private final
focal_class.original_string: private final List<String> parseResultAndErrorSummaryLines;
focal_class.type: List<String>
focal_class.var_name: parseResultAndErrorSummaryLines
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/hpo/PhenotypeDotHpoaFileWriter.java
focal_class.identifier: PhenotypeDotHpoaFileWriter
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.factory(Ontology ont,
                                                     String smallFileDirectoryPath,
                                                     String orphaPhenotypeXMLpath,
                                                     String orphaInheritanceXMLpath,
                                                     String outpath,
                                                     boolean toler,
                                                     boolean merge_fr)
focal_class.full_signature: public static PhenotypeDotHpoaFileWriter factory(Ontology ont,
                                                     String smallFileDirectoryPath,
                                                     String orphaPhenotypeXMLpath,
                                                     String orphaInheritanceXMLpath,
                                                     String outpath,
                                                     boolean toler,
                                                     boolean merge_fr)
focal_class.identifier: factory
focal_class.modifiers: public static
focal_class.parameters: (Ontology ont,
                                                     String smallFileDirectoryPath,
                                                     String orphaPhenotypeXMLpath,
                                                     String orphaInheritanceXMLpath,
                                                     String outpath,
                                                     boolean toler,
                                                     boolean merge_fr)
focal_class.return: PhenotypeDotHpoaFileWriter
focal_class.signature: PhenotypeDotHpoaFileWriter factory(Ontology ont,
                                                     String smallFileDirectoryPath,
                                                     String orphaPhenotypeXMLpath,
                                                     String orphaInheritanceXMLpath,
                                                     String outpath,
                                                     boolean toler,
                                                     boolean merge_fr)
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.PhenotypeDotHpoaFileWriter(Ontology ont,
                                       String smallFileDirectoryPath,
                                       String orphaPhenotypeXMLpath,
                                       String orphaInheritanceXMLpath,
                                       String outpath,
                                       boolean toler,
                                       boolean merge_fr)
focal_class.full_signature: private  PhenotypeDotHpoaFileWriter(Ontology ont,
                                       String smallFileDirectoryPath,
                                       String orphaPhenotypeXMLpath,
                                       String orphaInheritanceXMLpath,
                                       String outpath,
                                       boolean toler,
                                       boolean merge_fr)
focal_class.identifier: PhenotypeDotHpoaFileWriter
focal_class.modifiers: private
focal_class.parameters: (Ontology ont,
                                       String smallFileDirectoryPath,
                                       String orphaPhenotypeXMLpath,
                                       String orphaInheritanceXMLpath,
                                       String outpath,
                                       boolean toler,
                                       boolean merge_fr)
focal_class.signature:  PhenotypeDotHpoaFileWriter(Ontology ont,
                                       String smallFileDirectoryPath,
                                       String orphaPhenotypeXMLpath,
                                       String orphaInheritanceXMLpath,
                                       String outpath,
                                       boolean toler,
                                       boolean merge_fr)
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.setNumberOfDiseasesForHeader()
focal_class.full_signature: private void setNumberOfDiseasesForHeader()
focal_class.identifier: setNumberOfDiseasesForHeader
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setNumberOfDiseasesForHeader()
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.setOntologyMetadata(Map<String, String> meta)
focal_class.full_signature: private void setOntologyMetadata(Map<String, String> meta)
focal_class.identifier: setOntologyMetadata
focal_class.modifiers: private
focal_class.parameters: (Map<String, String> meta)
focal_class.return: void
focal_class.signature: void setOntologyMetadata(Map<String, String> meta)
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.getDate()
focal_class.full_signature: private String getDate()
focal_class.identifier: getDate
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getDate()
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.outputBigFile()
focal_class.full_signature: public void outputBigFile()
focal_class.identifier: outputBigFile
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void outputBigFile()
focal_class.class_method_signature: PhenotypeDotHpoaFileWriter.getHeaderLine()
focal_class.full_signature: static String getHeaderLine()
focal_class.identifier: getHeaderLine
focal_class.modifiers: static
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getHeaderLine()
focal_method.body: static String getHeaderLine() {
      String[] fields = {"DatabaseID",
        "DiseaseName",
        "Qualifier",
        "HPO_ID",
        "Reference",
        "Evidence",
        "Onset",
        "Frequency",
        "Sex",
        "Modifier",
        "Aspect",
        "Biocuration"};
      return "#" + String.join("\t", fields);
    }
focal_method.class_method_signature: PhenotypeDotHpoaFileWriter.getHeaderLine()
focal_method.full_signature: static String getHeaderLine()
focal_method.identifier: getHeaderLine
focal_method.invocations: join
focal_method.modifiers: static
focal_method.parameters: ()
focal_method.return: String
focal_method.signature: String getHeaderLine()