@Test
public void testAddMemberReplicaForShard() {
configuration.addMemberReplicaForShard("people-1", MEMBER_2);
String shardName = configuration.getShardNameForModule("people");
assertEquals("ModuleShardName", "people-1", shardName);
ShardStrategy shardStrategy = configuration.getStrategyForModule("people");
assertEquals("ModuleStrategy", ModuleShardStrategy.class, shardStrategy.getClass());
Collection<MemberName> members = configuration.getMembersFromShardName("people-1");
assertEquals("Members", ImmutableSortedSet.of(MEMBER_1, MEMBER_2),
ImmutableSortedSet.copyOf(members));
configuration.addMemberReplicaForShard("non-existent", MEMBER_2);
Set<String> shardNames = configuration.getAllShardNames();
assertEquals("ShardNames", ImmutableSortedSet.of("people-1", "cars-1", "test-1", "default"),
ImmutableSortedSet.copyOf(shardNames));
}
java类com.google.common.collect.ImmutableSortedSet的实例源码
ConfigurationImplTest.java 文件源码
项目：hashsdn-controller
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FibonacciFitter.java 文件源码
项目：java-monitoring-client-library
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/**
* Returns a new {@link CustomFitter} with bounds corresponding to the Fibonacci sequence.
*
* @param maxBucketSize the maximum bucket size to create (rounded down to the nearest Fibonacci
* number)
* @throws IllegalArgumentException if {@code maxBucketSize <= 0}
*/
public static CustomFitter create(long maxBucketSize) {
checkArgument(maxBucketSize > 0, "maxBucketSize must be greater than 0");
ImmutableSortedSet.Builder<Double> boundaries = ImmutableSortedSet.naturalOrder();
boundaries.add(Double.valueOf(0));
long i = 1;
long j = 2;
long k = 3;
while (i <= maxBucketSize) {
boundaries.add(Double.valueOf(i));
i = j;
j = k;
k = i + j;
}
return CustomFitter.create(boundaries.build());
}
ExponentialFitter.java 文件源码
项目：java-monitoring-client-library
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/**
* Create a new {@link ExponentialFitter}.
*
* @param numFiniteIntervals the number of intervals, excluding the underflow and overflow
* intervals
* @param base the base of the exponent
* @param scale a multiplicative factor for the exponential function
* @throws IllegalArgumentException if {@code numFiniteIntervals <= 0}, {@code width <= 0} or
* {@code base <= 1}
*/
public static ExponentialFitter create(int numFiniteIntervals, double base, double scale) {
checkArgument(numFiniteIntervals > 0, "numFiniteIntervals must be greater than 0");
checkArgument(scale != 0, "scale must not be 0");
checkArgument(base > 1, "base must be greater than 1");
checkDouble(base);
checkDouble(scale);
ImmutableSortedSet.Builder<Double> boundaries = ImmutableSortedSet.naturalOrder();
for (int i = 0; i < numFiniteIntervals + 1; i++) {
boundaries.add(scale * Math.pow(base, i));
}
return new AutoValue_ExponentialFitter(base, scale, boundaries.build());
}
ImmutableConverter.java 文件源码
项目：andbg
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@Nonnull
public SortedSet<ImmutableItem> toSortedSet(@Nonnull Comparator<? super ImmutableItem> comparator,
@Nullable final SortedSet<? extends Item> sortedSet) {
if (sortedSet == null || sortedSet.size() == 0) {
return ImmutableSortedSet.of();
}
@SuppressWarnings("unchecked")
ImmutableItem[] newItems = (ImmutableItem[])new Object[sortedSet.size()];
int index = 0;
for (Item item: sortedSet) {
newItems[index++] = makeImmutable(item);
}
return ArraySortedSet.of(comparator, newItems);
}
GoOboParserTest.java 文件源码
项目：ontolib
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@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());
}
HpoOboParserTest.java 文件源码
项目：ontolib
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@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());
}
MpoOboParserTest.java 文件源码
项目：ontolib
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@Test
public void testParseHpoHead() throws IOException {
final MpoOboParser parser = new MpoOboParser(mpoHeadFile, true);
final MpoOntology ontology = parser.parse();
assertEquals(
"ImmutableDirectedGraph [edgeLists={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=1]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=3]], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=3]]]}, edgeCount=3]",
ontology.getGraph().toString());
assertEquals(
"[ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000368], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075]]",
ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString());
assertEquals(
"{ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]=MPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], altTermIds=[], name=mammalian phenotype, definition=the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000368]=MPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000368]], name=abnormal coat/hair pigmentation, definition=irregular or unusual pigmentation of the hair, comment=null, subsets=[Europhenome_Terms, IMPC, Sanger_Terms], synonyms=[ImmutableTermSynonym [value=abnormal coat color, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=abnormal hair pigmentation, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=coat: color anomalies, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=MGI:2173541, description=null, trailingModifiers=null]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=MPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], altTermIds=[], name=pigmentation phenotype, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188]=MPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188], altTermIds=[], name=hyperpigmentation, definition=excess of pigment in any or all tissues or a part of a tissue, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075]=MPOTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075], altTermIds=[ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000368]], name=abnormal coat/hair pigmentation, definition=irregular or unusual pigmentation of the hair, comment=null, subsets=[Europhenome_Terms, IMPC, Sanger_Terms], synonyms=[ImmutableTermSynonym [value=abnormal coat color, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=abnormal hair pigmentation, scope=EXACT, synonymTypeName=null, termXrefs=[]], ImmutableTermSynonym [value=coat: color anomalies, scope=EXACT, synonymTypeName=null, termXrefs=[]]], obsolete=false, createdBy=null, creationDate=null, xrefs=[ImmutableDbxref [name=MGI:2173541, description=null, trailingModifiers=null]]]}",
ImmutableSortedMap.copyOf(ontology.getTermMap()).toString());
assertEquals(
"{1=MpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=1, relationQualifier=IS_A], 2=MpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001188], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=2, relationQualifier=IS_A], 3=MpoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0002075], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], id=3, relationQualifier=IS_A]}",
ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString());
assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]",
ontology.getRootTermId().toString());
assertEquals("{data-version=releases/2017-06-05}", ontology.getMetaInfo().toString());
}
UberphenoOboParserTest.java 文件源码
项目：ontolib
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@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, xrefs=[]], 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, xrefs=[]], 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, xrefs=[]], 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, xrefs=[]], 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, xrefs=[]]}",
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());
}
ConfigurationImplTest.java 文件源码
项目：hashsdn-controller
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@Test
public void testRemoveMemberReplicaForShard() {
configuration.removeMemberReplicaForShard("default", MEMBER_2);
String shardName = configuration.getShardNameForModule("default");
assertEquals("ModuleShardName", "default", shardName);
ShardStrategy shardStrategy = configuration.getStrategyForModule("default");
assertNull("ModuleStrategy", shardStrategy);
Collection<MemberName> members = configuration.getMembersFromShardName("default");
assertEquals("Members", ImmutableSortedSet.of(MEMBER_1, MEMBER_3),
ImmutableSortedSet.copyOf(members));
configuration.removeMemberReplicaForShard("non-existent", MEMBER_2);
Set<String> shardNames = configuration.getAllShardNames();
assertEquals("ShardNames", ImmutableSortedSet.of("people-1", "cars-1", "test-1", "default"),
ImmutableSortedSet.copyOf(shardNames));
}
PropertySourcesProcessor.java 文件源码
项目：apollo-custom
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protected void initializePropertySources() {
if (environment.getPropertySources().contains(APOLLO_PROPERTY_SOURCE_NAME)) {
//already initialized
return;
}
CompositePropertySource composite = new CompositePropertySource(APOLLO_PROPERTY_SOURCE_NAME);
//sort by order asc
ImmutableSortedSet<Integer> orders = ImmutableSortedSet.copyOf(NAMESPACE_NAMES.keySet());
Iterator<Integer> iterator = orders.iterator();
while (iterator.hasNext()) {
int order = iterator.next();
for (String namespace : NAMESPACE_NAMES.get(order)) {
Config config = ConfigService.getConfig(namespace);
composite.addPropertySource(new ConfigPropertySource(namespace, config));
}
}
environment.getPropertySources().addFirst(composite);
}
MapCommands.java 文件源码
项目：ProjectAres
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@Command(
aliases = {"maplist", "maps", "ml"},
desc = "Shows the maps that are currently loaded",
usage = "[page]",
min = 0,
max = 1,
help = "Shows all the maps that are currently loaded including ones that are not in the rotation."
)
@CommandPermissions("pgm.maplist")
public static void maplist(CommandContext args, final CommandSender sender) throws CommandException {
final Set<PGMMap> maps = ImmutableSortedSet.copyOf(new PGMMap.DisplayOrder(), PGM.getMatchManager().getMaps());
new PrettyPaginatedResult<PGMMap>(PGMTranslations.get().t("command.map.mapList.title", sender)) {
@Override public String format(PGMMap map, int index) {
return (index + 1) + ". " + map.getInfo().getShortDescription(sender);
}
}.display(new BukkitWrappedCommandSender(sender), maps, args.getInteger(0, 1) /* page */);
}
NullAwayNativeModels.java 文件源码
项目：NullAway
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static void guavaStuff() {
Collection<String> c = null;
Object o = null;
// BUG: Diagnostic contains: passing @Nullable parameter 'c' where @NonNull is required
ImmutableList.builder().addAll(c).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'o' where @NonNull is required
ImmutableList.builder().add(o).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'c' where @NonNull is required
ImmutableSet.builder().addAll(c).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'o' where @NonNull is required
ImmutableSet.builder().add(o).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'c' where @NonNull is required
ImmutableSortedSet.builder().addAll(c).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'o' where @NonNull is required
ImmutableSortedSet.builder().add(o).build();
// BUG: Diagnostic contains: passing @Nullable parameter 'c' where @NonNull is required
Iterables.getFirst(c, "hi");
}
ImportOrderer.java 文件源码
项目：javaide
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private String reorderedImportsString(ImmutableSortedSet<Import> imports) {
assert !imports.isEmpty();
Import firstImport = imports.iterator().next();
// Pretend that the first import was preceded by another import of the same kind
// (static or non-static), so we don't insert a newline there.
boolean lastWasStatic = firstImport.isStatic;
StringBuilder sb = new StringBuilder();
for (Import thisImport : imports) {
if (lastWasStatic && !thisImport.isStatic) {
// Blank line between static and non-static imports.
sb.append(lineSeparator);
}
lastWasStatic = thisImport.isStatic;
sb.append(thisImport);
}
return sb.toString();
}
ParentChildIndexFieldData.java 文件源码
项目：Elasticsearch
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public ParentChildIndexFieldData(Index index, Settings indexSettings, MappedFieldType.Names fieldNames,
FieldDataType fieldDataType, IndexFieldDataCache cache, MapperService mapperService,
CircuitBreakerService breakerService) {
super(index, indexSettings, fieldNames, fieldDataType, cache);
this.breakerService = breakerService;
if (Version.indexCreated(indexSettings).before(Version.V_2_0_0_beta1)) {
parentTypes = new TreeSet<>();
for (DocumentMapper documentMapper : mapperService.docMappers(false)) {
beforeCreate(documentMapper);
}
mapperService.addTypeListener(this);
} else {
ImmutableSortedSet.Builder<String> builder = ImmutableSortedSet.naturalOrder();
for (DocumentMapper mapper : mapperService.docMappers(false)) {
ParentFieldMapper parentFieldMapper = mapper.parentFieldMapper();
if (parentFieldMapper.active()) {
builder.add(parentFieldMapper.type());
}
}
parentTypes = builder.build();
}
}
GoOboParserTest.java 文件源码
项目：boqa
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@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());
}
HpoOboParserTest.java 文件源码
项目：boqa
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@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());
}
FieldEncryptorConfigTest.java 文件源码
项目：PACE
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@Test
public void readTest() throws IOException {
FieldEncryptorConfig expectedConfig = new FieldEncryptorConfigBuilder().setValueEncryptor(ValueEncryptor.AES_CBC).setProvider("SunJCE").setKeyLength(24)
.setEncryptUsingVisibility(false).setKeyId("keyId").setDestination(EntryField.COLUMN_FAMILY)
.setSources(ImmutableSortedSet.of(EntryField.ROW, EntryField.COLUMN_QUALIFIER, EntryField.COLUMN_FAMILY)).build();
FieldEncryptorConfig actualConfig = new FieldEncryptorConfigBuilder().readFromIni(getIni("config1.ini").get(EntryField.COLUMN_FAMILY.toString())).build();
assertThat("reading the ini file produces the correct configuration", actualConfig, hasSameFieldsAs(expectedConfig));
expectedConfig = new FieldEncryptorConfigBuilder().setValueEncryptor(ValueEncryptor.AES_CBC).setProvider("BC").setKeyLength(16)
.setEncryptUsingVisibility(true).setKeyId("AES_CBC").setDestination(EntryField.ROW).setSources(ImmutableSortedSet.of(EntryField.ROW)).build();
actualConfig = new FieldEncryptorConfigBuilder().readFromIni(getIni("config2.ini").get(EntryField.ROW.toString())).build();
assertThat("reading the ini file produces the correct configuration", actualConfig, hasSameFieldsAs(expectedConfig));
expectedConfig = new FieldEncryptorConfigBuilder().setValueEncryptor(ValueEncryptor.AES_CBC).setKeyLength(16).setEncryptUsingVisibility(true)
.setKeyId("AES_CBC").setDestination(EntryField.ROW).setSources(ImmutableSortedSet.of(EntryField.ROW)).build();
actualConfig = new FieldEncryptorConfigBuilder().readFromIni(getIni("config2WithoutDefaults.ini").get(EntryField.ROW.toString())).build();
assertThat("default values are correctly set", actualConfig, hasSameFieldsAs(expectedConfig));
expectedConfig = new FieldEncryptorConfigBuilder().setValueEncryptor(ValueEncryptor.AES_CBC).setProvider(null).setKeyLength(16)
.setEncryptUsingVisibility(false).setKeyId(ValueEncryptor.AES_CBC.toString()).setDestination(EntryField.VALUE)
.setSources(ImmutableSortedSet.of(EntryField.VALUE)).build();
actualConfig = new FieldEncryptorConfigBuilder().readFromIni(getIni("config3.ini").get(EntryField.VALUE.toString())).build();
assertThat("reading the ini file produces the correct configuration", actualConfig, hasSameFieldsAs(expectedConfig));
}
UberphenoOboParserTest.java 文件源码
项目：boqa
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@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());
}
NullPointerTesterTest.java 文件源码
项目：googles-monorepo-demo
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final void check() {
runTester().assertNonNullValues(
Gender.MALE,
Integer.valueOf(0), 0,
"", "",
ImmutableList.of(), ImmutableList.of(),
ImmutableMap.of(), ImmutableMap.of(),
ImmutableSet.of(), ImmutableSet.of(),
ImmutableSortedSet.of(), ImmutableSortedSet.of(),
ImmutableMultiset.of(), ImmutableMultiset.of(),
ImmutableMultimap.of(), ImmutableMultimap.of(),
ImmutableTable.of(), ImmutableTable.of());
}
BaseInstanceFactory.java 文件源码
项目：Reer
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@Override
public Set<ModelType<? extends PUBLIC>> getSupportedTypes() {
ImmutableSortedSet.Builder<ModelType<? extends PUBLIC>> supportedTypes = ImmutableSortedSet.orderedBy(ModelTypes.<PUBLIC>displayOrder());
for (TypeRegistration<?> registration : registrations.values()) {
if (registration.isConstructible()) {
supportedTypes.add(registration.publicType);
}
}
return supportedTypes.build();
}
StructSchemaExtractionStrategySupport.java 文件源码
项目：Reer
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private static String propertyDescription(ModelSchemaExtractionContext<?> parentContext, ModelProperty<?> property) {
if (property.getDeclaredBy().size() == 1 && property.getDeclaredBy().contains(parentContext.getType())) {
return String.format("property '%s'", property.getName());
} else {
ImmutableSortedSet<String> declaredBy = ImmutableSortedSet.copyOf(Iterables.transform(property.getDeclaredBy(), Functions.toStringFunction()));
return String.format("property '%s' declared by %s", property.getName(), Joiner.on(", ").join(declaredBy));
}
}
ModelPropertyExtractionContext.java 文件源码
项目：Reer
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public Set<ModelType<?>> getDeclaredBy() {
ImmutableSortedSet.Builder<ModelType<?>> declaredBy = new ImmutableSortedSet.Builder<ModelType<?>>(Ordering.usingToString());
for (PropertyAccessorExtractionContext accessor : accessors.values()) {
for (Method method : accessor.getDeclaringMethods()) {
declaredBy.add(ModelType.declaringType(method));
}
}
return declaredBy.build();
}
CollectionUtils.java 文件源码
项目：andbg
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@Nonnull
private static <T> SortedSet<? extends T> toNaturalSortedSet(@Nonnull Collection<? extends T> collection) {
if (isNaturalSortedSet(collection)) {
return (SortedSet<? extends T>)collection;
}
return ImmutableSortedSet.copyOf(collection);
}
DefaultNodeInitializerRegistry.java 文件源码
项目：Reer
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private ModelTypeInitializationException canNotConstructTypeException(NodeInitializerContext<?> context) {
ImmutableSortedSet.Builder<ModelType<?>> constructibleTypes = ImmutableSortedSet.orderedBy(ModelTypes.displayOrder());
for (NodeInitializerExtractionStrategy extractor : additionalStrategies) {
for (ModelType<?> constructibleType : extractor.supportedTypes()) {
if (context.getConstraints().isSatisfiedBy(constructibleType)) {
constructibleTypes.add(constructibleType);
}
}
}
return new ModelTypeInitializationException(context, schemaStore, ScalarTypes.TYPES, constructibleTypes.build());
}
DefaultTaskClassValidatorExtractor.java 文件源码
项目：Reer
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@Override
public TaskClassValidator extractValidator(Class<? extends Task> type) {
ImmutableSet.Builder<TaskPropertyInfo> validatedPropertiesBuilder = ImmutableSet.builder();
ImmutableSet.Builder<String> nonAnnotatedPropertiesBuilder = ImmutableSortedSet.naturalOrder();
Queue<TypeEntry> queue = new ArrayDeque<TypeEntry>();
queue.add(new TypeEntry(null, type));
while (!queue.isEmpty()) {
TypeEntry entry = queue.remove();
parseProperties(entry.parent, entry.type, validatedPropertiesBuilder, nonAnnotatedPropertiesBuilder, queue);
}
return new TaskClassValidator(validatedPropertiesBuilder.build(), nonAnnotatedPropertiesBuilder.build());
}
TaskPropertyUtils.java 文件源码
项目：Reer
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public static <T extends TaskFilePropertySpec> SortedSet<T> collectFileProperties(String displayName, Iterator<? extends T> fileProperties) {
Set<String> names = Sets.newHashSet();
ImmutableSortedSet.Builder<T> builder = ImmutableSortedSet.naturalOrder();
while (fileProperties.hasNext()) {
T propertySpec = fileProperties.next();
String propertyName = propertySpec.getPropertyName();
if (!names.add(propertyName)) {
throw new IllegalArgumentException(String.format("Multiple %s file properties with name '%s'", displayName, propertyName));
}
builder.add(propertySpec);
}
return builder.build();
}
SetGenerators.java 文件源码
项目：googles-monorepo-demo
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@Override
protected List<String> create(String[] elements) {
Comparator<String> comparator = createExplicitComparator(elements);
ImmutableSortedSet.Builder<String> builder = ImmutableSortedSet.orderedBy(comparator);
builder.add(BEFORE_FIRST);
builder.add(BEFORE_FIRST_2);
builder.add(elements);
builder.add(AFTER_LAST);
builder.add(AFTER_LAST_2);
return builder
.build()
.subSet(BEFORE_FIRST_2, AFTER_LAST_2)
.asList()
.subList(1, elements.length + 1);
}
NullPointerTesterTest.java 文件源码
项目：googles-monorepo-demo
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@SuppressWarnings("unused") // called by NullPointerTester
public void checkDefaultValuesForTheseTypes(
Gender gender,
Integer integer, int i,
String string, CharSequence charSequence,
List<String> list,
ImmutableList<Integer> immutableList,
Map<String, Integer> map,
ImmutableMap<String, String> immutableMap,
Set<String> set,
ImmutableSet<Integer> immutableSet,
SortedSet<Number> sortedSet,
ImmutableSortedSet<Number> immutableSortedSet,
Multiset<String> multiset,
ImmutableMultiset<Integer> immutableMultiset,
Multimap<String, Integer> multimap,
ImmutableMultimap<String, Integer> immutableMultimap,
Table<String, Integer, Exception> table,
ImmutableTable<Integer, String, Exception> immutableTable) {
calledWith(
gender,
integer, i,
string, charSequence,
list, immutableList,
map, immutableMap,
set, immutableSet,
sortedSet, immutableSortedSet,
multiset, immutableMultiset,
multimap, immutableMultimap,
table, immutableTable);
}
DefaultTest.java 文件源码
项目：GitHub
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@Test
public void defArray() {
ImmutableDefaultArray a1 = ImmutableDefaultArray.builder().build();
int[] array = a1.prop();
int[] nextArray = a1.prop();
check(array != nextArray);
check(a1.ints() instanceof ImmutableSortedSet);
}
LinearFitter.java 文件源码
项目：java-monitoring-client-library
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/**
* Create a new {@link LinearFitter}.
*
* @param numFiniteIntervals the number of intervals, excluding the underflow and overflow
* intervals
* @param width the width of each interval
* @param offset the start value of the first interval
* @throws IllegalArgumentException if {@code numFiniteIntervals <= 0} or {@code width <= 0}
*/
public static LinearFitter create(int numFiniteIntervals, double width, double offset) {
checkArgument(numFiniteIntervals > 0, "numFiniteIntervals must be greater than 0");
checkArgument(width > 0, "width must be greater than 0");
checkDouble(offset);
ImmutableSortedSet.Builder<Double> boundaries = ImmutableSortedSet.naturalOrder();
for (int i = 0; i < numFiniteIntervals + 1; i++) {
boundaries.add(width * i + offset);
}
return new AutoValue_LinearFitter(width, offset, boundaries.build());
}
