owlsim-v3
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Published
20 hours ago •
monarch-initiative
monarch-initiative
Building javadoc fails due to missing parameter descriptions
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] owlsim ............................................. SUCCESS [ 1.848 s]
[INFO] owlsim-core ........................................ FAILURE [ 5.273 s]
[INFO] owlsim REST services ............................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8.506 s
[INFO] Finished at: 2018-04-10T10:49:26+01:00
[INFO] Final Memory: 21M/309M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:3.0.0:javadoc (default-cli) on project owlsim-core: An error has occurred in Javadoc report generation:
[ERROR] Exit code: 1 - /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:126: warning: no description for @param
[ERROR] * @param owlOntology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:127: warning: no description for @param
[ERROR] * @param owlDataOntology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:128: warning: no description for @param
[ERROR] * @param rf
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:129: warning: no description for @return
[ERROR] * @return
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:131: warning: no @param for curieUtil
[ERROR] public static BMKnowledgeBase create(OWLOntology owlOntology, OWLOntology owlDataOntology, OWLReasonerFactory rf, CurieUtil curieUtil) {
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:615: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:624: warning: no description for @param
[ERROR] * @param index
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:632: warning: no description for @param
[ERROR] * @param index
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:640: warning: no description for @param
[ERROR] * @param cix
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:678: warning: no description for @param
[ERROR] * @param index
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:708: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:753: warning: no description for @param
[ERROR] * @param c
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:761: warning: no description for @param
[ERROR] * @param c
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:769: warning: no description for @param
[ERROR] * @param c
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:770: warning: no description for @param
[ERROR] * @param isDirect
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:778: warning: no description for @param
[ERROR] * @param clsSet
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:833: warning: no description for @param
[ERROR] * @param clsIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:845: warning: no description for @param
[ERROR] * @param clsIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:857: warning: no description for @param
[ERROR] * @param clsIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:869: warning: no description for @param
[ERROR] * @param clsIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:881: warning: no description for @param
[ERROR] * @param i
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:889: warning: no description for @param
[ERROR] * @param i
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:897: warning: no description for @param
[ERROR] * @param i
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:898: error: @param name not found
[ERROR] * @param classFilter
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:898: warning: no description for @param
[ERROR] * @param classFilter
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:902: warning: no @param for c
[ERROR] protected EWAHCompressedBitmap getFilteredDirectTypesBM(OWLNamedIndividual i, OWLClass c) {
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:907: warning: no description for @param
[ERROR] * @param i
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:908: warning: no description for @param
[ERROR] * @param isDirect
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:916: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:925: warning: no description for @param
[ERROR] * @param individualIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:942: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:951: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:960: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:969: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:992: warning: no description for @param
[ERROR] * @param obj
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:75: error: bad use of '>'
[ERROR] * Note: there can be >1 class in a node
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:89: error: bad use of '>'
[ERROR] * Note: there can be >1 individual in a node
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:96: warning: no description for @param
[ERROR] * @param individualId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:97: warning: no description for @return
[ERROR] * @return
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:107: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:115: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:121: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:127: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:133: warning: no description for @param
[ERROR] * @param classIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:139: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:146: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:153: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:159: warning: no description for @param
[ERROR] * @param classIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:165: warning: no description for @param
[ERROR] * @param classIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:171: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:177: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:183: error: @param name not found
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:183: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:186: warning: no @param for classesBM
[ERROR] public EWAHCompressedBitmap getSuperClassesBM(EWAHCompressedBitmap classesBM);
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:189: warning: no description for @param
[ERROR] * @param classIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:195: warning: no description for @param
[ERROR] * @param classIds
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:215: error: malformed HTML
[ERROR] * @return map between Type class index and 0<weight<=100, where probability = weight/100
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:215: error: malformed HTML
[ERROR] * @return map between Type class index and 0<weight<=100, where probability = weight/100
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:220: warning: no description for @param
[ERROR] * @param itemId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:226: warning: no description for @param
[ERROR] * @param itemId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:234: warning: no description for @return
[ERROR] * @return
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:263: warning: no description for @param
[ERROR] * @param index
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:269: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:280: warning: no description for @param
[ERROR] * @param index
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:291: warning: no description for @param
[ERROR] * @param bm
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:301: warning: no description for @param
[ERROR] * @param ont
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:327: warning: no description for @param
[ERROR] * @param individualId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:333: warning: no description for @param
[ERROR] * @param individualId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:334: warning: no description for @param
[ERROR] * @param property
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:359: warning: no @param for entity
[ERROR] public String resolveIri(String entity);
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:81: warning: no description for @param
[ERROR] * @param owlOntology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:84: warning: no description for @param
[ERROR] * @param reasonerFactory
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java:86: warning: no @param for curieUtil
[ERROR] public BMKnowledgeBaseOWLAPIImpl(OWLOntology owlOntology, OWLOntology owlDataOntology, OWLReasonerFactory reasonerFactory, CurieUtil curieUtil) {
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/ClassFrequencyStoreImpl.java:16: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/ClassFrequencyStoreImpl.java:24: warning: no description for @param
[ERROR] * @param classId
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/ClassFrequencyStoreImpl.java:25: warning: no description for @param
[ERROR] * @param isStrict
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/CURIEMapperImpl.java:17: warning: no description for @param
[ERROR] * @param iri
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/CURIEMapperImpl.java:25: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/CURIEMapper.java:14: warning: no description for @param
[ERROR] * @param iri
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/CURIEMapper.java:20: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:46: warning: no description for @param
[ERROR] * @param label
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:58: warning: no description for @param
[ERROR] * @param label
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:60: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:71: warning: no description for @param
[ERROR] * @param labels
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:73: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:86: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:98: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:100: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:111: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:122: error: malformed HTML
[ERROR] * Initialize label<->id mappings using an OWLOntology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:122: error: bad use of '>'
[ERROR] * Initialize label<->id mappings using an OWLOntology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:126: warning: no description for @param
[ERROR] * @param ontology
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:14: warning: no description for @param
[ERROR] * @param label
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:20: warning: no description for @param
[ERROR] * @param label
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:22: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:27: warning: no description for @param
[ERROR] * @param labels
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:29: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:34: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:40: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:42: warning: no description for @throws
[ERROR] * @throws NonUniqueLabelException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/LabelMapper.java:47: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/LabelMapperImpl.java:39: warning: no description for @param
[ERROR] * @param curieMapper
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:16: error: header used out of sequence: <H4>
[ERROR] * <h4>KB formalism</h4>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:30: error: self-closing element not allowed
[ERROR] * <br/>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:35: error: self-closing element not allowed
[ERROR] * <br/>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:39: error: self-closing element not allowed
[ERROR] * <br/>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:42: error: malformed HTML
[ERROR] * informativeness. if <code>Ix(C1) < Ix(C2)</code>, then <code>Informativeness(C1) =< Informativeness(C2)</code>.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java:42: error: malformed HTML
[ERROR] * informativeness. if <code>Ix(C1) < Ix(C2)</code>, then <code>Informativeness(C1) =< Informativeness(C2)</code>.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/GraphUtils.java:29: warning: no description for @param
[ERROR] * @param kb
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/NonUniqueLabelException.java:19: warning: no description for @param
[ERROR] * @param label
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/NonUniqueLabelException.java:20: warning: no description for @param
[ERROR] * @param ids
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/UnindexedClassException.java:15: warning: no description for @param
[ERROR] * @param id
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/ewah/EWAHKnowledgeBaseStore.java:60: warning: no description for @param
[ERROR] * @param clsIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/ewah/EWAHKnowledgeBaseStore.java:76: warning: no description for @param
[ERROR] * @param clsIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java:42: error: malformed HTML
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java:42: error: bad use of '>'
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java:17: error: malformed HTML
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java:17: error: bad use of '>'
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java:19: error: malformed HTML
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java:19: error: bad use of '>'
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OWLLoader.java:115: error: @param name not found
[ERROR] * @param path
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OWLLoader.java:127: error: @param name not found
[ERROR] * @param path
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:52: error: @param name not found
[ERROR] * @param <code>ci</code>childClassIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:52: error: unexpected end tag: </code>
[ERROR] * @param <code>ci</code>childClassIndex
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/SimplePairwiseConditionalProbabilityIndex.java:20: error: @param name not found
[ERROR] * @param parentIndex - integer encoding D
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/impl/ThreeStateConditionalProbabilityIndex.java:21: error: bad HTML entity
[ERROR] * The calculation for the on & unknown state combos is the same as for
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:11: error: invalid entity ∈
[ERROR] * the <i>states</i> of P1..Pn, where Pi_s ∈ S.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:17: error: reference not found
[ERROR] * <li>{@link ThreeStateConditionalProbabilityIndex} S={on,unknown,off}
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:22: error: malformed HTML
[ERROR] * created, psi, an integer 0<=i<|S|^n, where representing each possible state of each parent.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/cpt/ConditionalProbabilityIndex.java:22: error: malformed HTML
[ERROR] * created, psi, an integer 0<=i<|S|^n, where representing each possible state of each parent.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java:52: error: block element not allowed within inline element <code>: pre
[ERROR] * <pre>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java:54: error: malformed HTML
[ERROR] * Pr( C=on | S1, ..., Sn) = <-- syntactic sugar
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java:296: error: @param name not found
[ERROR] * @param targetProfileBM
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateProfileMatcher.java:116: error: bad use of '>'
[ERROR] * When k>1, will make use of the k least frequent annotations in probabilistic calculation
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java:27: error: malformed HTML
[ERROR] * Pr(Child = on | P) = SUM[0<i<3^|P|] { Pr(Child=on | Si) * Pr(Si) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java:27: error: malformed HTML
[ERROR] * Pr(Child = on | P) = SUM[0<i<3^|P|] { Pr(Child=on | Si) * Pr(Si) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java:246: error: @param name not found
[ERROR] * @param targetProfileBM
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/CoAnnotationStats.java:73: error: malformed HTML
[ERROR] * Returns a list of <Class id - Count> pairs representing all co-annotated classes with the
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/CoAnnotationStats.java:73: error: bad use of '>'
[ERROR] * Returns a list of <Class id - Count> pairs representing all co-annotated classes with the
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/ICDistribution.java:96: error: malformed HTML
[ERROR] * the tTest is unable to be performed due to insufficient values (length < 2),
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/ICDistributionValue.java:4: error: malformed HTML
[ERROR] * This is a proxy for a set of <x,y> coordinates,
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/ICDistributionValue.java:4: error: bad use of '>'
[ERROR] * This is a proxy for a set of <x,y> coordinates,
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/model/match/impl/GridMatchImpl.java:26: error: @param name not found
[ERROR] * @param qmatchArr
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/model/match/MatchSet.java:33: error: malformed HTML
[ERROR] * @return all matches <= rank
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/model/match/MatchSet.java:44: error: @param name not found
[ERROR] * @param createMatch
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/model/match/impl/WeightedQueryImpl.java:18: error: invalid use of @return
[ERROR] * @return map between classId and weight
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:44: error: reference not found
[ERROR] * @throws NoReasonerFoundException if no reasoner has been set
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:45: error: reference not found
[ERROR] * @throws UnknownOWLClassException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:46: error: reference not found
[ERROR] * @see createAnnotationsForAttributeSet
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:58: error: reference not found
[ERROR] * {@link HashSets}, and will only retrieve unique attribute sets.</p>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:58: error: unexpected end tag: </p>
[ERROR] * {@link HashSets}, and will only retrieve unique attribute sets.</p>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:60: error: @param name not found
[ERROR] * @param insts
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:62: error: reference not found
[ERROR] * @throws NoReasonerFoundException if no reasoner has been set.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:63: error: reference not found
[ERROR] * @throws UnknownOWLClassException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:64: error: reference not found
[ERROR] * @see createAnnotationsForAttributeSet
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:74: error: reference not found
[ERROR] * {@link HashSets}, and will only retrieve unique attribute sets.</p>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:78: error: reference not found
[ERROR] * @throws NoReasonerFoundException
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/AbstractSimulatedData.java:23: error: @param name not found
[ERROR] * @param g
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/AbstractSimulatedData.java:24: error: @param name not found
[ERROR] * @param owlsim
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/BackgroundData.java:19: error: reference not found
[ERROR] * for significance testing of {@link Match}es resulting from ProfileMatchers. <br />
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/BackgroundData.java:19: error: self-closing element not allowed
[ERROR] * for significance testing of {@link Match}es resulting from ProfileMatchers. <br />
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/BackgroundData.java:20: error: reference not found
[ERROR] * For speed of subsequent analysis, proper {@link OWLIndividuals} are not used;
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RandomChooseNSimulatedData.java:123: error: bad use of '>'
[ERROR] * If {@code setLength} >= {@code atts.size()} , it will generate a random
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RandomChooseNSimulatedData.java:125: error: @param name not found
[ERROR] * @param atts
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RandomChooseNSimulatedData.java:22: error: malformed HTML
[ERROR] * it will return as many unique sets as possible <= numSets.</li>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RemoveByCategorySimulatedData.java:123: error: unknown tag: false
[ERROR] * category, then set this to {@false}.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/SimulatedData.java:14: error: reference not found
[ERROR] * derived data for all or a subset of individuals loaded in a provided {@link BMKnowledgeBase}.
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/package-info.java:23: error: bad use of '>'
[ERROR] * M/br>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:3: error: self-closing element not allowed
[ERROR] * <br/>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:6: error: invalid entity ∈
[ERROR] * CA(a,b) = { x | x ∈ Anc*(a), x ∈ Anc*(b) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:6: error: invalid entity ∈
[ERROR] * CA(a,b) = { x | x ∈ Anc*(a), x ∈ Anc*(b) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:7: error: invalid entity ∈
[ERROR] * MICA(a,b) = { x | x ∈ MICA(a,b), not exists y, y ∈ MICA(a,b), IC(y) > IC(x) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:7: error: invalid entity ∈
[ERROR] * MICA(a,b) = { x | x ∈ MICA(a,b), not exists y, y ∈ MICA(a,b), IC(y) > IC(x) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/mica/package-info.java:7: error: bad use of '>'
[ERROR] * MICA(a,b) = { x | x ∈ MICA(a,b), not exists y, y ∈ MICA(a,b), IC(y) > IC(x) }
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologyLoadException.java:4: error: malformed HTML
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR] /ws/owlsim-v3/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologyLoadException.java:4: error: bad use of '>'
[ERROR] * @author Jules Jacobsen <[email protected]>
[ERROR] ^
[ERROR]
