public AbstractStructSchema( ModelType<T> type, Iterable<ModelProperty<?>> properties, Iterable<WeaklyTypeReferencingMethod<?, ?>> nonPropertyMethods, Iterable<ModelSchemaAspect> aspects ) { super(type); ImmutableSortedMap.Builder<String, ModelProperty<?>> builder = ImmutableSortedMap.naturalOrder(); for (ModelProperty<?> property : properties) { builder.put(property.getName(), property); } this.properties = builder.build(); this.nonPropertyMethods = ImmutableSet.copyOf(nonPropertyMethods); this.aspects = Maps.uniqueIndex(aspects, new Function<ModelSchemaAspect, Class<? extends ModelSchemaAspect>>() { @Override public Class<? extends ModelSchemaAspect> apply(ModelSchemaAspect aspect) { return aspect.getClass(); } }); }
private <T> ImmutableSortedMap<String, ManagedProperty<?>> collectManagedProperties(StructBindingExtractionContext<T> extractionContext, Map<String, Multimap<PropertyAccessorType, StructMethodBinding>> propertyBindings) { ImmutableSortedMap.Builder<String, ManagedProperty<?>> managedPropertiesBuilder = ImmutableSortedMap.naturalOrder(); for (Map.Entry<String, Multimap<PropertyAccessorType, StructMethodBinding>> propertyEntry : propertyBindings.entrySet()) { String propertyName = propertyEntry.getKey(); Multimap<PropertyAccessorType, StructMethodBinding> accessorBindings = propertyEntry.getValue(); if (isManagedProperty(extractionContext, propertyName, accessorBindings)) { if (hasSetter(accessorBindings.keySet()) && !hasGetter(accessorBindings.keySet())) { extractionContext.add(propertyName, "it must both have an abstract getter and a setter"); continue; } ModelType<?> propertyType = determineManagedPropertyType(extractionContext, propertyName, accessorBindings); ModelSchema<?> propertySchema = schemaStore.getSchema(propertyType); managedPropertiesBuilder.put(propertyName, createManagedProperty(extractionContext, propertyName, propertySchema, accessorBindings)); } } return managedPropertiesBuilder.build(); }
protected DefaultStructBindings( StructSchema<T> publicSchema, Iterable<? extends StructSchema<?>> declaredViewSchemas, Iterable<? extends StructSchema<?>> implementedViewSchemas, @Nullable StructSchema<?> delegateSchema, Map<String, ManagedProperty<?>> managedProperties, Iterable<StructMethodBinding> methodBindings ) { this.publicSchema = publicSchema; this.declaredViewSchemas = ImmutableSet.copyOf(declaredViewSchemas); this.implementedViewSchemas = ImmutableSet.copyOf(implementedViewSchemas); this.delegateSchema = delegateSchema; this.managedProperties = ImmutableSortedMap.copyOf(managedProperties, Ordering.natural()); this.methodBindings = ImmutableList.copyOf(methodBindings); }
LongPositions(Iterable<? extends Object> elements, final int bitPerLong) { this.elements = ImmutableList.copyOf(elements); checkArgument(bitPerLong <= BITS_IN_LONG, bitPerLong); for (int i = 0; i < this.elements.size(); i++) { positions.put( this.elements.get(i), new BitPosition( i / bitPerLong, i % bitPerLong)); } this.longPositions = ImmutableSortedMap.copyOf( Maps.transformEntries( Multimaps.index(positions.values(), ToLongIndex.FUNCTION).asMap(), new Maps.EntryTransformer<Integer, Collection<BitPosition>, LongSet>() { @Override public LongSet transformEntry(Integer key, Collection<BitPosition> position) { return new LongSet(key, position); } })); }
@Inject ScoreKBPAgainstERE( final Parameters params, final Map<String, ScoringEventObserver<DocLevelEventArg, DocLevelEventArg>> scoringEventObservers, final ResponsesAndLinkingFromEREExtractor responsesAndLinkingFromEREExtractor, ResponsesAndLinkingFromKBPExtractorFactory responsesAndLinkingFromKBPExtractorFactory, @DocIDsToScoreP Set<Symbol> docIdsToScore, @KeyFileMapP Map<Symbol, File> keyFilesMap, Predicate<DocLevelEventArg> inScopePredicate, @PermitMissingSystemDocsP boolean permitMissingSystemDocuments) { this.params = checkNotNull(params); // we use a sorted map because the binding of plugins may be non-deterministic this.scoringEventObservers = ImmutableSortedMap.copyOf(scoringEventObservers); this.responsesAndLinkingFromEREExtractor = checkNotNull(responsesAndLinkingFromEREExtractor); this.responsesAndLinkingFromKBPExtractorFactory = responsesAndLinkingFromKBPExtractorFactory; this.docIDsToScore = ImmutableSet.copyOf(docIdsToScore); this.goldDocIDToFileMap = ImmutableMap.copyOf(keyFilesMap); this.inScopePredicate = inScopePredicate; this.permitMissingSystemDocuments = permitMissingSystemDocuments; }
public ThriftStructMetadata( String structName, Map<String, String> idlAnnotations, Type structType, Type builderType, MetadataType metadataType, Optional<ThriftMethodInjection> builderMethod, List<String> documentation, List<ThriftFieldMetadata> fields, Optional<ThriftConstructorInjection> constructorInjection, List<ThriftMethodInjection> methodInjections) { this.builderType = builderType; this.builderMethod = requireNonNull(builderMethod, "builderMethod is null"); this.structName = requireNonNull(structName, "structName is null"); this.idlAnnotations = requireNonNull(idlAnnotations, "idlAnnotations is null"); this.metadataType = requireNonNull(metadataType, "metadataType is null"); this.structType = requireNonNull(structType, "structType is null"); this.constructorInjection = requireNonNull(constructorInjection, "constructorInjection is null"); this.documentation = ImmutableList.copyOf(requireNonNull(documentation, "documentation is null")); this.fields = ImmutableSortedMap.copyOf(uniqueIndex(requireNonNull(fields, "fields is null"), ThriftFieldMetadata::getId)); this.methodInjections = ImmutableList.copyOf(requireNonNull(methodInjections, "methodInjections is null")); }
@Test public void testParseUberphenoHead() throws IOException { final UberphenoOboParser parser = new UberphenoOboParser(uberphenoHeadFile, true); final UberphenoOntology ontology = parser.parse(); assertEquals( "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4]], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3]]]}, edgeCount=4]", ontology.getGraph().toString()); assertEquals( "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]]", ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString()); assertEquals( "{ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], altTermIds=[], name=All, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], altTermIds=[], name=mammalian phenotype, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], altTermIds=[], name=pigmentation phenotype, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], altTermIds=[], name=UBERPHENO_ROOT, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], altTermIds=[], name=abnormal(ly) quality zebrafish anatomical entity, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null]}", ImmutableSortedMap.copyOf(ontology.getTermMap()).toString()); assertEquals( "{1=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1, relationQualifier=IS_A], 2=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2, relationQualifier=IS_A], 3=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3, relationQualifier=IS_A], 4=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4, relationQualifier=IS_A]}", ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString()); assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]", ontology.getRootTermId().toString()); assertEquals("{date=20:01:2012 06:00}", ontology.getMetaInfo().toString()); }
/** * Constructor. * * @param metaInfo {@link ImmutableMap} with meta information. * @param graph Graph to use for underlying structure. * @param rootTermId Root node's {@link TermId}. * @param nonObsoleteTermIds {@link Collection} of {@link TermId}s of non-obsolete terms. * @param obsoleteTermIds {@link Collection} of {@link TermId}s of obsolete terms. * @param termMap Mapping from {@link TermId} to <code>T</code>. * @param relationMap Mapping from numeric edge Id to <code>R</code>. */ public ImmutableOntology(ImmutableSortedMap<String, String> metaInfo, ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>> graph, TermId rootTermId, Collection<? extends TermId> nonObsoleteTermIds, Collection<? extends TermId> obsoleteTermIds, ImmutableMap<TermId, T> termMap, ImmutableMap<Integer, R> relationMap) { this.metaInfo = metaInfo; this.graph = graph; this.rootTermId = rootTermId; this.termMap = termMap; this.nonObsoleteTermIds = ImmutableSet.copyOf(nonObsoleteTermIds); this.obsoleteTermIds = ImmutableSet.copyOf(obsoleteTermIds); this.allTermIds = ImmutableSet.copyOf(Sets.union(this.nonObsoleteTermIds, this.obsoleteTermIds)); this.relationMap = relationMap; this.precomputedAncestors = precomputeAncestors(); }
private WriteBufferStats createWriteBufferStats(final String cfName, final String hostname) { return new WriteBufferStats() { private ImmutableSortedMap<String, String> m_tags = ImmutableSortedMap.<String, String>naturalOrder() .put("host", hostname) .put("buffer", cfName) .build(); @Override public void saveWriteSize(int pendingWrites) { putInternalDataPoint("kairosdb.datastore.write_size", m_tags, m_longDataPointFactory.createDataPoint(System.currentTimeMillis(), pendingWrites)); } }; }
/** * Parse OBO file into {@link HpoOntology} object. * * @return {@link HpoOntology} from parsing OBO file. * @throws IOException In case of problems with file I/O. */ @SuppressWarnings("unchecked") public GoOntology parse() throws IOException { final OboImmutableOntologyLoader<GoTerm, GoTermRelation> loader = new OboImmutableOntologyLoader<>(oboFile, debug); final GoOboFactory factory = new GoOboFactory(); final ImmutableOntology<GoTerm, GoTermRelation> o = loader.load(factory); // Convert ImmutableOntology into GoOntology. The casts here are ugly and require the // @SuppressWarnings above but this saves us one factory layer of indirection. return new GoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(), (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(), o.getNonObsoleteTermIds(), o.getObsoleteTermIds(), (ImmutableMap<TermId, GoTerm>) o.getTermMap(), (ImmutableMap<Integer, GoTermRelation>) o.getRelationMap()); }
/** * Parse OBO file into {@link MpoOntology} object. * * @return {@link MpoOntology} from parsing OBO file. * @throws IOException In case of problems with file I/O. */ @SuppressWarnings("unchecked") public MpoOntology parse() throws IOException { final OboImmutableOntologyLoader<MpoTerm, MpoTermRelation> loader = new OboImmutableOntologyLoader<>(oboFile, debug); final MpoOboFactory factory = new MpoOboFactory(); final ImmutableOntology<MpoTerm, MpoTermRelation> o = loader.load(factory); // Convert ImmutableOntology into Mpontology. The casts here are ugly and require the // @SuppressWarnings above but this saves us one factory layer of indirection. return new MpoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(), (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(), o.getNonObsoleteTermIds(), o.getObsoleteTermIds(), (ImmutableMap<TermId, MpoTerm>) o.getTermMap(), (ImmutableMap<Integer, MpoTermRelation>) o.getRelationMap()); }
/** * Parse OBO file into {@link UberphenoOntology} object. * * @return {@link UberphenoOntology} from parsing OBO file. * @throws IOException In case of problems with file I/O. */ @SuppressWarnings("unchecked") @Override public UberphenoOntology parse() throws IOException { final OboImmutableOntologyLoader<UberphenoTerm, UberphenoTermRelation> loader = new OboImmutableOntologyLoader<>(oboFile, debug); final UberphenoOboFactory factory = new UberphenoOboFactory(); final ImmutableOntology<UberphenoTerm, UberphenoTermRelation> o = loader.load(factory); // Convert ImmutableOntology into Uberphenontology. The casts here are ugly and require the // @SuppressWarnings above but this saves us one factory layer of indirection. return new UberphenoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(), (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(), o.getNonObsoleteTermIds(), o.getObsoleteTermIds(), (ImmutableMap<TermId, UberphenoTerm>) o.getTermMap(), (ImmutableMap<Integer, UberphenoTermRelation>) o.getRelationMap()); }
@Test public void testParseHpoHead() throws IOException { final GoOboParser parser = new GoOboParser(goHeadFile, true); final GoOntology ontology = parser.parse(); assertEquals( "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3]]]}, edgeCount=3]", ontology.getGraph().toString()); assertEquals( "[ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000004], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005554], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0007582], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008372]]", ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString()); assertThat(ImmutableSortedMap.copyOf(ontology.getTermMap()).toString(), startsWith("{ImmutableTermId")); assertThat(ImmutableSortedMap.copyOf(ontology.getTermMap()).toString(), endsWith("description=null, trailingModifiers=null]]]}")); assertEquals( "{1=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1, relationQualifier=IS_A], 2=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2, relationQualifier=IS_A], 3=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3, relationQualifier=IS_A]}", ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString()); assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000]", ontology.getRootTermId().toString()); assertEquals( "{data-version=releases/2017-06-16, remark=Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0]}", ontology.getMetaInfo().toString()); }
@Test public void testParseHpoHead() throws IOException { final HpoOboParser parser = new HpoOboParser(hpoHeadFile, true); final HpoOntology ontology = parser.parse(); assertEquals( "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3]], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4]]]}, edgeCount=4]", ontology.getGraph().toString()); assertEquals( "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]]", ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString()); assertEquals( "{ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], altTermIds=[], name=All, definition=null, comment=Root of all terms in the Human Phenotype Ontology., subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=UMLS:C0444868, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=UMLS:C1708511, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:258211005, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0441748, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C4020899, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], altTermIds=[], name=Phenotypic abnormality, definition=A phenotypic abnormality., comment=This is the root of the phenotypic abnormality subontology of the HPO., subsets=[], synonyms=[ImmutableTermSynonym [value=Organ abnormality, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=UMLS:C4021819, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:258211005, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0441748, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C4020899, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=UMLS:C1708511, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=UMLS:C1708511, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:263681008, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0443147, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=SNOMEDCT_US:258211005, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C0441748, description=null, trailingModifiers=null], ImmutableDbxref [name=UMLS:C4020899, description=null, trailingModifiers=null]]]}", ImmutableSortedMap.copyOf(ontology.getTermMap()).toString()); assertEquals( "{1=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1, relationQualifier=IS_A], 2=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2, relationQualifier=IS_A], 3=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3, relationQualifier=IS_A], 4=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4, relationQualifier=IS_A]}", ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString()); assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]", ontology.getRootTermId().toString()); assertEquals( "{data-version=releases/2017-04-13, saved-by=Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al.}", ontology.getMetaInfo().toString()); }
public SaveAsDataPointAggregator(DataPointGroup innerDataPointGroup) { m_innerDataPointGroup = innerDataPointGroup; ImmutableSortedMap.Builder<String, String> mapBuilder = ImmutableSortedMap.<String, String>naturalOrder(); mapBuilder.putAll(m_tags); if (m_addSavedFrom) mapBuilder.put("saved_from", innerDataPointGroup.getName()); for (String innerTag : innerDataPointGroup.getTagNames()) { Set<String> tagValues = innerDataPointGroup.getTagValues(innerTag); if (m_tagsToKeep.contains(innerTag) && (tagValues.size() == 1)) mapBuilder.put(innerTag, tagValues.iterator().next()); } m_groupTags = mapBuilder.build(); }
/** * Determines the discount in value for distant regions */ public ImmutableSortedMap<Integer, BigDecimal> drawDistanceDiscounts(MRVMWorld world, MRVMRegionsMap.Region home, UniformDistributionRNG rng) { ImmutableSortedMap.Builder<Integer, BigDecimal> distanceDiscount = ImmutableSortedMap.naturalOrder(); distanceDiscount.put(0, BigDecimal.ONE); int maxDistance = world.getRegionsMap().getLongestShortestPath(home); for (int i = 1; i <= maxDistance; i++) { double exponent = exponentFactor * i * (-1); double gamma = Math.pow(base, exponent); Preconditions.checkState(gamma >= 0 && gamma <= 1, "Invalid Gamma, some of the calculation parameters have unallowed values"); BigDecimal roundedGamma = BigDecimal.valueOf(gamma).setScale(5, BigDecimal.ROUND_HALF_DOWN); distanceDiscount.put(i, roundedGamma); } return distanceDiscount.build(); }
private static ImmutableSortedMap<Integer, BigDecimal> buildGammaMap(Map<Integer, BigDecimal> gammaInput) { ImmutableSortedMap.Builder<Integer, BigDecimal> mapBuilder = ImmutableSortedMap.naturalOrder(); SortedMap<Integer, BigDecimal> sortedInput = new TreeMap<>(gammaInput); Preconditions.checkArgument(sortedInput.firstKey() == 1, "Gamma Values must (exclusively) be specified for quantities 1 and (optionally) higher", sortedInput); Preconditions.checkArgument(sortedInput.lastKey().equals(sortedInput.size()), "" + "Gamma Values must be specified for all capacities in {0, ..., k_{max}}, where k_{max} > 0 is any natural number > 0", sortedInput); for (Entry<Integer, BigDecimal> inputGammaEntry : sortedInput.entrySet()) { Preconditions.checkArgument(inputGammaEntry.getValue().compareTo(BigDecimal.ZERO) >= 0, "Gamma must not be negative", inputGammaEntry); mapBuilder.put(inputGammaEntry); } return mapBuilder.build(); }
/** * Constructs a new PieceWiseLinear function with a restricted domain interval * @param cornerPoints A map with <i>key = x-values</i> and <i> value = y-values</i>. * The map has to include all corner points of the function, including lower and upper end of domain. <br> * */ public ContinuousPiecewiseLinearFunction(Map<BigDecimal, BigDecimal> cornerPoints) { // Sort the incoming corner points by their SortedMap<BigDecimal, BigDecimal> sortedCornerPoints = new TreeMap<>(cornerPoints); ImmutableSortedMap.Builder<BigDecimal, LinearFunction> linearFunctionsBuilder = ImmutableSortedMap.naturalOrder(); Iterator<Entry<BigDecimal, BigDecimal>> entryIterator = sortedCornerPoints.entrySet().iterator(); Entry<BigDecimal, BigDecimal> lowerEntry = entryIterator.next(); lowestX = lowerEntry.getKey(); while (entryIterator.hasNext()) { Entry<BigDecimal, BigDecimal> upperEntry = entryIterator.next(); if (lowerEntry.getKey().compareTo(upperEntry.getKey()) == 0) { // Skip linear function where the domain is empty // TODO log this } else { LinearFunction linearFunction = new LinearFunction(lowerEntry.getKey(), lowerEntry.getValue(), upperEntry.getKey(), upperEntry.getValue()); linearFunctionsBuilder.put(upperEntry.getKey(), linearFunction); lowerEntry = upperEntry; } } linearFunctions = linearFunctionsBuilder.build(); }
/** * Parse OBO file into {@link HpoOntology} object. * * @return {@link HpoOntology} from parsing OBO file. * @throws IOException In case of problems with file I/O. */ @SuppressWarnings("unchecked") public HpoOntology parse() throws IOException { final OboImmutableOntologyLoader<HpoTerm, HpoTermRelation> loader = new OboImmutableOntologyLoader<>(oboFile, debug); final HpoOboFactory factory = new HpoOboFactory(); final ImmutableOntology<HpoTerm, HpoTermRelation> o = loader.load(factory); // Convert ImmutableOntology into HPOntology. The casts here are ugly and require the // @SuppressWarnings above but this saves us one factory layer of indirection. return new HpoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(), (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(), o.getNonObsoleteTermIds(), o.getObsoleteTermIds(), (ImmutableMap<TermId, HpoTerm>) o.getTermMap(), (ImmutableMap<Integer, HpoTermRelation>) o.getRelationMap()); }
/** * Parse OBO file into {@link UphenoOntology} object. * * @return {@link UphenoOntology} from parsing OBO file. * @throws IOException In case of problems with file I/O. */ @SuppressWarnings("unchecked") public UphenoOntology parse() throws IOException { final OboImmutableOntologyLoader<UphenoTerm, UphenoTermRelation> loader = new OboImmutableOntologyLoader<>(oboFile, debug); final UphenoOboFactory factory = new UphenoOboFactory(); final ImmutableOntology<UphenoTerm, UphenoTermRelation> o = loader.load(factory); // Convert ImmutableOntology into UberphenoOntology. The casts here are ugly and require the // @SuppressWarnings above but this saves us one factory layer of indirection. return new UphenoOntology((ImmutableSortedMap<String, String>) o.getMetaInfo(), (ImmutableDirectedGraph<TermId, ImmutableEdge<TermId>>) o.getGraph(), o.getRootTermId(), o.getNonObsoleteTermIds(), o.getObsoleteTermIds(), (ImmutableMap<TermId, UphenoTerm>) o.getTermMap(), (ImmutableMap<Integer, UphenoTermRelation>) o.getRelationMap()); }
@Test public void testParseHpoHead() throws IOException { final GoOboParser parser = new GoOboParser(goHeadFile, true); final GoOntology ontology = parser.parse(); assertEquals( "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3]]]}, edgeCount=3]", ontology.getGraph().toString()); assertEquals( "[ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000004], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005554], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0007582], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008372]]", ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString()); assertThat(ImmutableSortedMap.copyOf(ontology.getTermMap()).toString(), startsWith("{ImmutableTermId")); assertThat(ImmutableSortedMap.copyOf(ontology.getTermMap()).toString(), endsWith("createdBy=null, creationDate=null]}")); assertEquals( "{1=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0003674], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=1, relationQualifier=IS_A], 2=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0005575], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=2, relationQualifier=IS_A], 3=GoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0008150], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000], id=3, relationQualifier=IS_A]}", ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString()); assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=GO], id=0000000]", ontology.getRootTermId().toString()); assertEquals( "{data-version=releases/2017-06-16, remark=Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0]}", ontology.getMetaInfo().toString()); }
@Test public void testParseHpoHead() throws IOException { final HpoOboParser parser = new HpoOboParser(hpoHeadFile, true); final HpoOntology ontology = parser.parse(); assertEquals( "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3]], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4]]]}, edgeCount=4]", ontology.getGraph().toString()); assertEquals( "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]]", ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString()); assertEquals( "{ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], altTermIds=[], name=All, definition=null, comment=Root of all terms in the Human Phenotype Ontology., subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], altTermIds=[], name=Phenotypic abnormality, definition=A phenotypic abnormality., comment=This is the root of the phenotypic abnormality subontology of the HPO., subsets=[], synonyms=[ImmutableTermSynonym [value=Organ abnormality, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001453], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001461]], name=Mode of inheritance, definition=The pattern in which a particular genetic trait or disorder is passed from one generation to the next., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Inheritance, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001415], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001447], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001448], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001451], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001455], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001456], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001463]], name=Autosomal dominant inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal dominant, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal dominant form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal dominant type, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]]], obsolete=false, createdBy=null, creationDate=null], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]=HPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001416], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0001526]], name=Autosomal recessive inheritance, definition=A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)., comment=null, subsets=[], synonyms=[ImmutableTermSynonym [value=Autosomal recessive, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=Autosomal recessive form, scope=RELATED, synonymTypeName=null, termXrefs=[ImmutableTermXref [id=null, description=null]]], ImmutableTermSynonym [value=Autosomal recessive predisposition, scope=RELATED, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null]}", ImmutableSortedMap.copyOf(ontology.getTermMap()).toString()); assertEquals( "{1=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=1, relationQualifier=IS_A], 2=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000006], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=2, relationQualifier=IS_A], 3=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000007], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], id=3, relationQualifier=IS_A], 4=HpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000118], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], id=4, relationQualifier=IS_A]}", ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString()); assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]", ontology.getRootTermId().toString()); assertEquals( "{data-version=releases/2017-04-13, saved-by=Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al.}", ontology.getMetaInfo().toString()); }
<T, D> StructBindings<T> extract(ModelType<T> publicType, Iterable<? extends ModelType<?>> internalViewTypes, ModelType<D> delegateType) { if (delegateType != null && Modifier.isAbstract(delegateType.getConcreteClass().getModifiers())) { throw new InvalidManagedTypeException(String.format("Type '%s' is not a valid managed type: delegate type must be null or a non-abstract type instead of '%s'.", publicType.getDisplayName(), delegateType.getDisplayName())); } Set<ModelType<?>> implementedViews = collectImplementedViews(publicType, internalViewTypes, delegateType); StructSchema<T> publicSchema = getStructSchema(publicType); Iterable<StructSchema<?>> declaredViewSchemas = getStructSchemas(Iterables.concat(Collections.singleton(publicType), internalViewTypes)); Iterable<StructSchema<?>> implementedSchemas = getStructSchemas(implementedViews); StructSchema<D> delegateSchema = delegateType == null ? null : getStructSchema(delegateType); StructBindingExtractionContext<T> extractionContext = new StructBindingExtractionContext<T>(publicSchema, implementedSchemas, delegateSchema); if (!(publicSchema instanceof RuleSourceSchema)) { validateTypeHierarchy(extractionContext, publicType); for (ModelType<?> internalViewType : internalViewTypes) { validateTypeHierarchy(extractionContext, internalViewType); } } Map<String, Multimap<PropertyAccessorType, StructMethodBinding>> propertyBindings = Maps.newTreeMap(); Set<StructMethodBinding> methodBindings = collectMethodBindings(extractionContext, propertyBindings); ImmutableSortedMap<String, ManagedProperty<?>> managedProperties = collectManagedProperties(extractionContext, propertyBindings); if (extractionContext.problems.hasProblems()) { throw new InvalidManagedTypeException(extractionContext.problems.format()); } return new DefaultStructBindings<T>( publicSchema, declaredViewSchemas, implementedSchemas, delegateSchema, managedProperties, methodBindings ); }
@Override public Map<String, FileCollectionSnapshot> getInputFilesSnapshot() { if (inputFilesSnapshot == null) { ImmutableSortedMap.Builder<String, FileCollectionSnapshot> builder = ImmutableSortedMap.naturalOrder(); for (Map.Entry<String, Long> entry : inputFilesSnapshotIds.entrySet()) { builder.put(entry.getKey(), snapshotRepository.get(entry.getValue())); } inputFilesSnapshot = builder.build(); } return inputFilesSnapshot; }
@Override public void putDataPoint(String metricName, ImmutableSortedMap<String, String> tags, DataPoint dataPoint, int ttl) throws DatastoreException { DataPointKey key = new DataPointKey(metricName, tags, dataPoint.getApiDataType(), ttl); if ((m_prefixFilter != null) && (!metricName.startsWith(m_prefixFilter))) return; synchronized (m_mapLock) { m_dataPointMultimap.put(key, dataPoint); } }
public TaskExecutionSnapshot(String taskClass, ImmutableSet<String> cacheableOutputProperties, ImmutableSet<String> declaredOutputFilePaths, HashCode taskClassLoaderHash, HashCode taskActionsClassLoaderHash, Map<String, Object> inputProperties, ImmutableSortedMap<String, Long> inputFilesSnapshotIds, Long discoveredFilesSnapshotId, ImmutableSortedMap<String, Long> outputFilesSnapshotIds) { this.taskClass = taskClass; this.cacheableOutputProperties = cacheableOutputProperties; this.declaredOutputFilePaths = declaredOutputFilePaths; this.taskClassLoaderHash = taskClassLoaderHash; this.taskActionsClassLoaderHash = taskActionsClassLoaderHash; this.inputProperties = inputProperties; this.inputFilesSnapshotIds = inputFilesSnapshotIds; this.discoveredFilesSnapshotId = discoveredFilesSnapshotId; this.outputFilesSnapshotIds = outputFilesSnapshotIds; }
@Override public void run() { logger.info("Blast Server Running"); Stopwatch timer = Stopwatch.createStarted(); while (m_keepRunning) { long now = System.currentTimeMillis(); DataPoint dataPoint = m_longDataPointFactory.createDataPoint(now, 42); int row = RandomUtils.nextInt(0, m_numberOfRows); ImmutableSortedMap<String, String> tags = ImmutableSortedMap.of("row", String.valueOf(row), "host", "blast_server"); try { m_datastore.putDataPoint(m_metricName, tags, dataPoint, m_ttl); } catch (DatastoreException e) { e.printStackTrace(); } m_counter ++; if ((m_counter % 100000 == 0) && (timer.elapsed(TimeUnit.SECONDS) > m_durration)) m_keepRunning = false; } }
public static <T, K, V> Collector<T, ?, ImmutableSortedMap<K, V>> toSortedMap(Comparator<? super K> comparator, Function<? super T, ? extends K> keyMapper, Function<? super T, ? extends V> valueMapper) { return Collector.of( () -> new ImmutableSortedMap.Builder<K, V>(comparator), (builder, input) -> builder.put(keyMapper.apply(input), valueMapper.apply(input)), (l, r) -> l.putAll(r.build()), ImmutableSortedMap.Builder::build, Collector.Characteristics.UNORDERED ); }
@Inject HealthChecker( UriInfo uriInfo, ServiceMetadata serviceMetadata, Map<String, HealthDependency> healthDependencies) { this.uriInfo = uriInfo; this.serviceMetadata = serviceMetadata; this.healthDependencies = ImmutableSortedMap.copyOf(healthDependencies); }
protected AbstractReflectionThriftCodec(ThriftCodecManager manager, ThriftStructMetadata metadata) { this.metadata = metadata; ImmutableSortedMap.Builder<Short, ThriftCodec<?>> fields = ImmutableSortedMap.naturalOrder(); for (ThriftFieldMetadata fieldMetadata : metadata.getFields(THRIFT_FIELD)) { fields.put(fieldMetadata.getId(), manager.getCodec(fieldMetadata.getThriftType())); } this.fields = fields.build(); }
@Test public void testConstructTermAnnotationToLabelsMap() { Map<TermId, Collection<String>> map = ImmutableSortedMap .copyOf(TermAnnotations.constructTermAnnotationToLabelsMap(ontology, annotations)); assertEquals( "{ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=[two, one], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002]=[two, three, one], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000003]=[two, one], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000004]=[two, one], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]=[two, three, one]}", map.toString()); }
@Test public void testConstructTermLabelToAnnotationsMap() { Map<String, Collection<TermId>> map = ImmutableSortedMap .copyOf(TermAnnotations.constructTermLabelToAnnotationsMap(ontology, annotations)); assertEquals( "{one=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000003], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000004], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]], three=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]], two=[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000003], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000004], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]]}", map.toString()); }
private void putInternalDataPoint(String metricName, ImmutableSortedMap<String, String> tags, DataPoint dataPoint) { try { putDataPoint(metricName, tags, dataPoint, 0); } catch (DatastoreException e) { logger.error("", e); } }
@GwtIncompatible // SerializableTester public void testViewSerialization() { Map<String, Integer> map = ImmutableSortedMap.of("one", 1, "two", 2, "three", 3); SerializableTester.reserializeAndAssert(map.entrySet()); SerializableTester.reserializeAndAssert(map.keySet()); assertEquals(Lists.newArrayList(map.values()), Lists.newArrayList(SerializableTester.reserialize(map.values()))); }
public void putDataPoint(String metricName, ImmutableSortedMap<String, String> tags, DataPoint dataPoint, int ttl) throws DatastoreException { //Add to datastore first. m_datastore.putDataPoint(metricName, tags, dataPoint, ttl); for (DataPointListener dataPointListener : m_dataPointListeners) { dataPointListener.dataPoint(metricName, tags, dataPoint); } }
@Override public SortedMap<String, String> create(Entry<String, String>[] entries) { ImmutableSortedMap.Builder<String, String> builder = ImmutableSortedMap.naturalOrder(); for (Entry<String, String> entry : entries) { checkNotNull(entry); builder.put(entry.getKey(), entry.getValue()); } return builder.build(); }
