- g - Variable in class slib.graph.algo.extraction.rvf.RVF
-
- G - Interface in slib.graph.model.graph
-
Interface of a multi directed Graph defined as a set of vertices and a set of
oriented edges.
- GAction - Class in slib.graph.algo.extraction.utils
-
Class used to represent an action which is applicable to a graph.
- GAction(GActionType) - Constructor for class slib.graph.algo.extraction.utils.GAction
-
Build an instance of GAction considering the given type.
- GAction - Class in slib.graph.algo.utils
-
Class used to represent an action which is applicable to a graph.
- GAction(GActionType) - Constructor for class slib.graph.algo.utils.GAction
-
Build an instance of GAction considering the given type.
- GActionType - Enum in slib.graph.algo.extraction.utils
-
Enumeration used to represent the various types of actions which can be
applied to a graph.
- GActionType - Enum in slib.graph.algo.utils
-
Enumeration used to represent the various types of actions which can be
applied to a graph.
- GActionValidator - Class in slib.graph.algo.extraction.utils
-
Class used to validate if the configuration associated to a
GAction is valid.
- GActionValidator() - Constructor for class slib.graph.algo.extraction.utils.GActionValidator
-
- GActionValidator - Class in slib.graph.algo.utils
-
Class used to validate if the configuration associated to a
GAction is valid.
- GActionValidator() - Constructor for class slib.graph.algo.utils.GActionValidator
-
- GActionValidator - Class in slib.graph.io.util
-
- GActionValidator() - Constructor for class slib.graph.io.util.GActionValidator
-
- gamma - Variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
- gamma - Variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
- gamma_param_name - Static variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
- gamma_param_name - Static variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
- gConfGroupwise - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- gConfICs - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- gConfOperators - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- gConfPairwise - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- gConfQueries - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- GDataConf - Class in slib.graph.io.conf
-
- GDataConf(GFormat) - Constructor for class slib.graph.io.conf.GDataConf
-
- GDataConf(GFormat, String) - Constructor for class slib.graph.io.conf.GDataConf
-
- GDataValidator - Class in slib.graph.io.util
-
- GDataValidator() - Constructor for class slib.graph.io.util.GDataValidator
-
- GENE_PRODUCT_ISOFORM - Static variable in class slib.graph.io.loader.bio.gaf2.GraphLoader_GAF_2
-
- generic - Variable in class slib.tools.module.XML_ModuleConfLoader
-
- GenericConfBuilder - Class in slib.tools.module
-
- GenericConfBuilder() - Constructor for class slib.tools.module.GenericConfBuilder
-
- get(String) - Method in class slib.indexer.wordnet.IndexerWordNetBasic
-
- getAcceptedPredicates() - Method in interface slib.graph.model.graph.utils.WalkConstraint
-
Access to a view of the set of predicates (edge types) the walk consider
during edge evaluation.
- getAcceptedPredicates() - Method in class slib.graph.utils.WalkConstraintGeneric
-
- getAcceptedWalks_DIR_BOTH() - Method in interface slib.graph.model.graph.utils.WalkConstraint
-
- getAcceptedWalks_DIR_BOTH() - Method in class slib.graph.utils.WalkConstraintGeneric
-
- getAcceptedWalks_DIR_IN() - Method in interface slib.graph.model.graph.utils.WalkConstraint
-
Access to a view of the set of predicates which can be traversed from
target to source, i.e.
- getAcceptedWalks_DIR_IN() - Method in class slib.graph.utils.WalkConstraintGeneric
-
- getAcceptedWalks_DIR_OUT() - Method in interface slib.graph.model.graph.utils.WalkConstraint
-
Access to a view of the set of predicates which can be traversed from
source to target i.e.
- getAcceptedWalks_DIR_OUT() - Method in class slib.graph.utils.WalkConstraintGeneric
-
- getAction(String) - Static method in class slib.tools.smltoolkit.sm.cli.core.utils.ActionParamsUtils
-
- getActions() - Method in class slib.graph.io.conf.GraphConf
-
- getAllAncestorsExc() - Method in class slib.graph.algo.extraction.rvf.AncestorEngine
-
Compute the set of exclusive ancestors of all vertices contained in the
graph.
- getAllAncestorsInc() - Method in class slib.graph.algo.extraction.rvf.AncestorEngine
-
Compute the set of inclusive ancestors of all vertices contained in the
graph.
- getAllAncestorsInc() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to the inclusive ancestors for all classes.
- getAllDescendantsExc() - Method in class slib.graph.algo.extraction.rvf.DescendantEngine
-
Compute the set of exclusive descendants of all vertices contained in the
graph.
- getAllDescendantsInc() - Method in class slib.graph.algo.extraction.rvf.DescendantEngine
-
Compute the set of inclusive descendants of all vertices contained in the
graph.
- getAllDescendantsInc() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to a view of the inclusive descendants for all classes.
- getAllNbAncestorsInc() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Inclusive process
- getAllNbDescendantsInc() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute the number of inclusive descendants for all classes
- getAllNbReachableLeaves() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute for each class x the number classes which are leaves which are
subsumed by x.
- getAllRV() - Method in class slib.graph.algo.extraction.rvf.RVF_DAG
-
Compute the set of reachable vertices for each vertices contained in the
graph according to the specified constraint associated to the instance in
use.
- getAllRVClass() - Method in class slib.graph.algo.extraction.rvf.RVF_TAX
-
Compute for all vertices of the loaded graph, the set of vertices corresponding to classes which can be reach from them.
- getAllShortestPath(URI, GWS) - Method in class slib.sml.sm.core.engine.SM_Engine
-
CACHED
- getAncestorEngine() - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getAncestorsExc(URI) - Method in class slib.graph.algo.extraction.rvf.AncestorEngine
-
Compute the set of exclusive ancestors of a class.
- getAncestorsInc(URI) - Method in class slib.graph.algo.extraction.rvf.AncestorEngine
-
Compute the set of inclusive ancestors of a class.
- getAncestorsInc(Set<URI>) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute the union of the inclusive ancestors of a set of classes.
- getAncestorsInc(URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Give access to a view of the inclusive ancestors of a class.
- getAppCmdName() - Method in class slib.tools.module.ToolCmdHandlerCst
-
- getAppName() - Method in class slib.tools.module.ModuleCst
-
- getAssociatedDirection(URI) - Method in interface slib.graph.model.graph.utils.WalkConstraint
-
Return the direction associated to the given predicate the object admits
- getAssociatedDirection(URI) - Method in class slib.graph.utils.WalkConstraintGeneric
-
- getAssociatedURI() - Method in interface slib.indexer.URIDescription
-
- getAssociatedURI() - Method in class slib.indexer.URIDescriptionBasic
-
- getAttValue(Element, String) - Method in class slib.tools.module.XML_ModuleConfLoader
-
- getAverage() - Method in class slib.utils.impl.MatrixDouble
-
Return the average of contained valued.
- getBATCH_LIMIT() - Method in class slib.sml.smutils.SQLiteUtils
-
- getBATCH_LIMIT_MATRIX_LINE() - Method in class slib.sml.smutils.SQLiteUtils
-
- getBenchSize() - Method in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- getCachePairwiseResults() - Method in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- getCapacity() - Method in class slib.utils.threads.PoolLocker
-
- getClasses(G) - Static method in class slib.graph.algo.accessor.GraphAccessor
-
Return a set of URI corresponding to the classes of the graph.
- getClasses() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to the set of URI of the graph considered as classes.
- getClassName() - Method in class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Getter of the class name.
- getClassName() - Method in class slib.sml.sm.core.utils.SMconf
-
- getColumn(C) - Method in class slib.utils.impl.MatrixDouble
-
Return the column associated to the given element
- getColumn(Object) - Method in class slib.utils.impl.MatrixDynamic
-
- getColumnElements() - Method in class slib.utils.impl.MatrixDouble
-
- getContact() - Method in class slib.tools.module.ModuleCst
-
- getDAGRoots(G, WalkConstraint) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Root vertices (terminal vertices) are those of type CLASS which respect
the following restrictions :
must not contains an edges of
the given types and direction
Do not check if the graph is a DAG
- getDAGRoots(G, WalkConstraint) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Root vertices (terminal vertices) are those of type CLASS which respect
the following restrictions :
must not contains an edges of
the given types and direction
Do not check if the graph is a DAG
- getData() - Method in class slib.graph.io.conf.GraphConf
-
- getDebugMode() - Method in class slib.tools.module.ToolCmdHandlerCst
-
- getDefaultWeight() - Method in interface slib.graph.model.graph.weight.GWS
-
The default weight associated to an edge
- getDefaultWeight() - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- getDescendantEngine() - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getDescendantsExc(URI) - Method in class slib.graph.algo.extraction.rvf.DescendantEngine
-
Compute the set of exclusive descendants of a class.
- getDescendantsInc(URI) - Method in class slib.graph.algo.extraction.rvf.DescendantEngine
-
Compute the set of inclusive descendants of a class.
- getDescendantsInc(URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Give access to a view of the inclusive descendants of a class.
- getDescription(URI) - Method in class slib.indexer.IndexHash
-
Access to the description associated to a specific URI
- getDescription() - Method in class slib.tools.module.ModuleCst
-
- getDescriptions() - Method in interface slib.indexer.URIDescription
-
Access to the descriptions associated to the object
- getDescriptions() - Method in class slib.indexer.URIDescriptionBasic
-
- getDescriptorName() - Method in class slib.graph.io.loader.bio.mesh.MeshConcept
-
- getDescriptorName() - Method in class slib.indexer.mesh.MeshDescriptor
-
- getDescriptorUI() - Method in class slib.graph.io.loader.bio.mesh.MeshConcept
-
- getDescriptorUI() - Method in class slib.indexer.mesh.MeshDescriptor
-
- getDirectClass(URI) - Method in class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- getDirectClass(URI) - Method in interface slib.graph.algo.extraction.rvf.instances.InstancesAccessor
-
Method providing access to the classes annotating an instance.
- getDirectInstances(URI) - Method in class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- getDirectInstances(URI) - Method in interface slib.graph.algo.extraction.rvf.instances.InstancesAccessor
-
Access to a way to iterate through the set of instances considered as
direct instances of a class e.g.
- getDirectInstancesNumber(URI) - Method in class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- getDocFields() - Method in class slib.sml.sm.core.measures.corpus.VocContextMatrixBuilder
-
- getE() - Method in interface slib.graph.model.graph.G
-
Access to a view of the set of edges contained in the graph.
- getE(URI, Direction) - Method in interface slib.graph.model.graph.G
-
Access to a view of all edges involving a specific vertex considering a
particular direction.
- getE(URI) - Method in interface slib.graph.model.graph.G
-
Retrieve a view of all edges characterized by the specified URI
predicate.
- getE(Set<URI>) - Method in interface slib.graph.model.graph.G
-
Retrieve a view of all edges characterized by one of specified predicate
URIs.
- getE(URI, URI, Direction) - Method in interface slib.graph.model.graph.G
-
Retrieve a view of all edges of the graph characterized by the specified
constraint.
- getE(Set<URI>, URI, Direction) - Method in interface slib.graph.model.graph.G
-
Retrieve a view of all edges of the graph characterized by the
constraint.
- getE(URI, WalkConstraint) - Method in interface slib.graph.model.graph.G
-
Retrieve a view of all edges of the graph which can be reached from a
given vertex respecting the given constraint.
- getE() - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(URI) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(Set<URI>, URI, Direction) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(URI, URI, Direction) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(URI, Direction) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(Set<URI>) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getE(URI, WalkConstraint) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getExcludedEC() - Method in class slib.graph.io.loader.utils.filter.graph.gaf2.FilterGraph_GAF2
-
- getFilter(String) - Method in class slib.graph.io.loader.utils.filter.graph.repo.FilterRepository
-
- getFilters() - Method in class slib.graph.io.loader.utils.filter.graph.repo.FilterRepository
-
- getFlag() - Method in class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Getter of the flag.
- getFlag() - Method in class slib.sml.sm.core.utils.SMconf
-
- getFormat() - Method in class slib.graph.io.conf.GDataConf
-
- getGraph(URI) - Method in class slib.graph.model.impl.repo.GraphRepositoryMemory
-
- getGraph(URI) - Method in interface slib.graph.model.repo.GraphRepository
-
Retrieve a graph according to its URI.
- getGraph() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to the graph associated to the engine.
- getGraph() - Method in class slib.tools.smltoolkit.sm.cli.core.SmCli
-
- getGraphConfs() - Method in class slib.tools.module.XMLConfLoaderGeneric
-
- getHypoAncEx(URI, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
NOT_CACHED
- getiAccessor() - Method in class slib.tools.smltoolkit.sm.cli.core.SmCli
-
- getIC(ICconf, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Get the Information Content of a class.
- getIC_MICA(ICconf, URI, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Get the information content of the most informative common ancestor
(MICA) of two classes.
- getIC_results(ICconf) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to a view of the information content of all classes.
- getICconf() - Method in class slib.sml.sm.core.utils.SMconf
-
The IC configuration associated to the configuration.
- getIcConf() - Method in class slib.sml.sm.core.utils.SMconf
-
- getICconf(String) - Method in class slib.tools.smltoolkit.sm.cli.core.SmCli
-
- getId() - Method in class slib.graph.io.loader.utils.filter.graph.Filter
-
- getId() - Method in class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Getter of the id.
- getId() - Method in class slib.sml.sm.core.utils.SMconf
-
- getId() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getIndex() - Method in class slib.indexer.wordnet.IndexerWordNetBasic
-
- getInfile() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getInfo(String) - Method in class slib.sml.smutils.SQLiteUtils
-
Return info a specified database
- getInfo(String, String) - Method in class slib.sml.smutils.SQLiteUtils
-
Return info a specified table
- getInstance() - Static method in class slib.graph.io.loader.utils.filter.graph.repo.FilterRepository
-
- getInstance() - Static method in class slib.tools.module.GlobalConfPattern
-
- getInstances(G) - Static method in class slib.graph.algo.accessor.GraphAccessor
-
Return a set of URI corresponding to the instances of the graph, note
that instance.
- getInstances() - Method in class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- getInstances(URI) - Method in class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- getInstances() - Method in interface slib.graph.algo.extraction.rvf.instances.InstancesAccessor
-
Return a way to iterate over the collection of instances.
- getInstances(URI) - Method in interface slib.graph.algo.extraction.rvf.instances.InstancesAccessor
-
Access to a way to iterate over an instance of a class.
- getInstances() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to the set of URI of the graph considered as instances.
- getInternalStorage() - Method in class slib.sml.sm.core.measures.corpus.Matrix
-
- getInverse(WalkConstraint, boolean) - Static method in class slib.graph.utils.WalkConstraintUtils
-
Build a
WalkConstraint object corresponding to the inverse of the
current object.
- getJobSize() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- getK() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Knappe_2004
-
- getK() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Tversky_1977
-
- getKey() - Method in class slib.tools.ontofocus.core.utils.QueryEntryURI
-
- getKey() - Method in class slib.utils.impl.QueryEntry
-
- getKey() - Method in class slib.utils.Pair
-
- getLabel() - Method in class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Getter of the label.
- getLabel() - Method in class slib.sml.sm.core.utils.SMconf
-
- getLastEdge() - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
- getLastEdge() - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
- getLCAs(URI, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getLCAs(URI, URI) - Method in interface slib.sml.sm.core.utils.LCAFinder
-
Compute the set of Disjoint Common Ancestors of a pair of concepts The
processed graph do not require to be transitively reduced.
- getLCAs(URI, URI) - Method in class slib.sml.sm.core.utils.LCAFinderImpl
-
- getLine(boolean, Long) - Method in class slib.sml.smutils.ResultsMerger
-
- getLoad() - Method in class slib.utils.threads.PoolLocker
-
- getLoc() - Method in class slib.graph.io.conf.GDataConf
-
- getLogBase() - Method in class slib.sml.sm.core.metrics.utils.LogBasedMetric
-
- getLogBase() - Method in interface slib.sml.sm.core.metrics.utils.LogBasedMetricInterface
-
Getter of the log base associated to the metric.
- getMapping() - Method in class slib.indexer.IndexHash
-
Access to the Map which stores the description of each resource.
- getMatrix() - Method in class slib.sml.sm.core.measures.corpus.VocContextMatrixBuilder
-
- getMatrix() - Method in class slib.utils.impl.MatrixDouble
-
- getMatrixScore(Set<URI>, Set<URI>, SMconf) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute the matrix of similarity for two sets of vertex/concepts/classes.
- getMax() - Method in class slib.utils.impl.MatrixDouble
-
- getMax(HashMap<X, Integer>) - Static method in class slib.utils.impl.SetUtils
-
- getMaxColumn(C) - Method in class slib.utils.impl.MatrixDouble
-
- getMaxDepth() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to the maximal depth of a class in the underlying taxonomic graph.
- getMaxDepths() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Give access to a view of the maximal depth of all classes.
- getMaxDepthsDistribution() - Method in class slib.graph.algo.extraction.metric.DepthAnalyserAG
-
- getMaxDepthsDistribution() - Method in class slib.graph.algo.metric.DepthAnalyserAG
-
- getMaxLoadPoolWorker() - Method in class slib.utils.threads.ThreadManager
-
- getMaxRow(R) - Method in class slib.utils.impl.MatrixDouble
-
- getMaxThread() - Method in class slib.utils.threads.ThreadManager
-
- getMetric() - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- getMICA(ICconf, URI, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Get the most informative common ancestor (MICA) of two classes.
- getMin() - Method in class slib.utils.impl.MatrixDouble
-
Return the minimal value stored in the matrix
- getMinDepths() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Give access to a view of the minimal depth of all classes.
- getMinDepthsDistribution() - Method in class slib.graph.algo.extraction.metric.DepthAnalyserAG
-
- getMinDepthsDistribution() - Method in class slib.graph.algo.metric.DepthAnalyserAG
-
- getMinStrictPositiveDouble(Map<X, Double>) - Static method in class slib.sml.sm.core.utils.SMutils
-
Return the minimal positive value amon the values of the map (0 excluded)
- getMSA(URI, URI, GWS) - Method in class slib.sml.sm.core.engine.SM_Engine
-
NOT_CACHED
- getMSA_pekar_staab(URI, Map<URI, Double>, Map<URI, Double>, Set<URI>, Set<URI>, Dijkstra) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils.SimDagEdgeUtils
-
Compute the most specific ancestor considering Pekar and Staab 2002
formula to minimize i.e.
- getNamespace(String) - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- getNamespace(String) - Method in interface slib.graph.model.repo.URIFactory
-
- getNbColumns() - Method in class slib.utils.impl.MatrixDouble
-
- getNbColumns() - Method in class slib.utils.impl.MatrixDynamic
-
- getNbInstancesInferredPropFromCorpus(boolean) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Computes the number of instances which is associated to all the classes
which are defined in the graph (with inferences).
- getNbOccurrenceProp() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Topological propagation considering one occurrence per term
- getnbPathLeadingToAllVertex() - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getNbRows() - Method in class slib.utils.impl.MatrixDouble
-
- getNbRows() - Method in class slib.utils.impl.MatrixDynamic
-
- getNoAnnotAction() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getNoAnnotationScore() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getNoFoundAction() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getNoFoundScore() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getNumberEdges() - Method in interface slib.graph.model.graph.G
-
- getNumberEdges() - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getNumberQueries() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.QueryConceptsIterator
-
- getNumberQueries() - Method in class slib.utils.impl.QueryFileIterator
-
- getNumberQueries() - Method in interface slib.utils.impl.QueryIterator
-
- getNumberVertices() - Method in interface slib.graph.model.graph.G
-
Return the number of vertices
- getNumberVertices() - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getOpposite() - Method in enum slib.graph.model.graph.utils.Direction
-
Return the opposite direction of a particular Direction.
- getOptionOrder() - Method in class slib.tools.module.ToolCmdHandlerCst
-
- getOutfile() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getP_MICA(ICconf, URI, URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getPairwiseApproach(String) - Static method in class slib.sml.sm.core.utils.SMConstants
-
Return the id of the approach associated to the semantic measure flag
- getParam(String) - Method in class slib.utils.i.Conf
-
Return the value associated to the given parameter as an
Object.
- getParamAsDouble(String) - Method in class slib.utils.i.Conf
-
Return the value associated to the given parameter as a double value.
- getParamAsString(String) - Method in class slib.utils.i.Conf
-
Return the value associated to the given parameter as a
String.
- getParameter(String) - Method in interface slib.utils.i.Parametrable
-
- getParameter(String) - Method in class slib.utils.impl.ParametrableImpl
-
- getParams() - Method in class slib.utils.i.Conf
-
Getter of the Map storing the entry loaded in the configuration.
- getParams() - Method in interface slib.utils.i.Parametrable
-
- getParams() - Method in class slib.utils.impl.ParametrableImpl
-
Can be null
- getParents(URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Get the parents of a class, that is to say its direct ancestors.
- getPool() - Method in class slib.utils.threads.PoolWorker
-
- getPoolWorker(int) - Method in class slib.utils.threads.ThreadManager
-
- getPreferredDescription() - Method in interface slib.indexer.URIDescription
-
Access to the preferred description of the resource.
- getPreferredDescription() - Method in class slib.indexer.URIDescriptionBasic
-
- getProperty(String) - Method in class slib.utils.impl.OProperty
-
- getPropertyKeys() - Method in class slib.utils.impl.OProperty
-
- getReachableLeaves() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute for each class x the classes which are leaves which are subsumed
by x.
- getReachableLeaves(URI) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Compute for each class x the classes which are leaves which are subsumed
by x.
- getReference() - Method in class slib.tools.module.ModuleCst
-
- getRelationships() - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- getRoot() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Get the root of the taxonomic graph contained in the graph associated to
the engine.
- getRow(R) - Method in class slib.utils.impl.MatrixDouble
-
Return the row associated to the given element
- getRow(Object) - Method in class slib.utils.impl.MatrixDynamic
-
- getRowElements() - Method in class slib.utils.impl.MatrixDouble
-
- getRV(URI) - Method in class slib.graph.algo.extraction.rvf.RVF
-
Retrieve the set of reachable vertices RV from a specified vertex taking
into account the type of relationships associated to the current
instance.
- getRV(Set<URI>) - Method in class slib.graph.algo.extraction.rvf.RVF
-
Compute the set of reachable vertices for each vertices composing the
graph associated to the object considering the edge types loaded.
- getRVClass(URI) - Method in class slib.graph.algo.extraction.rvf.RVF_TAX
-
Compute the set of vertices corresponding to classes which can be reach from the given vertex.
- getRVnb(Set<URI>) - Method in class slib.graph.algo.extraction.rvf.RVF
-
Return the number of vertices reachable from all vertices composing the
graph associated to the instance.
- getSetValue(String) - Static method in class slib.tools.smltoolkit.sm.cli.core.utils.ActionParamsUtils
-
- getSetValue() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- getShortestPath(URI, URI, GWS) - Method in class slib.sml.sm.core.engine.SM_Engine
-
CACHED ! Be careful modification of RelTypes requires cache clearing
- getSingleton() - Static method in class slib.graph.model.impl.repo.GraphRepositoryMemory
-
- getSingleton() - Static method in class slib.graph.model.impl.repo.URIFactoryMemory
-
Access to the in-memory URI Factory.
- getSingleton() - Static method in class slib.utils.threads.ThreadManager
-
- getSkipped() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- getSmconf() - Method in class slib.tools.smltoolkit.sm.cli.profile.go.SmProfileGOHandler
-
- getSmconf() - Method in class slib.tools.smltoolkit.sm.cli.profile.mesh.SmProfileMeSHHandler
-
- getSource() - Method in interface slib.graph.model.graph.elements.E
-
- getSource() - Method in class slib.graph.model.impl.graph.elements.Edge
-
- getSum() - Method in class slib.utils.impl.MatrixDouble
-
Compute the sum of the values contained in the matrix.
- getSupportedFormat() - Static method in class slib.graph.io.loader.GraphLoaderGeneric
-
Access to the set of supported format.
- getTarget() - Method in interface slib.graph.model.graph.elements.E
-
- getTarget() - Method in class slib.graph.model.impl.graph.elements.Edge
-
- getTargetUriString() - Method in class slib.graph.io.loader.bio.obo.utils.OboRelationship
-
- getTaxonomicLeaves() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Access to a view of the set of leaves of the underlying taxonomic graph.
- getTaxonomicRoots(G) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Return the vertices which root the taxonomic graph.
- getTaxonomicRoots(G) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Return the vertices which root the taxonomic graph.
- getTaxons() - Method in class slib.graph.io.loader.utils.filter.graph.gaf2.FilterGraph_GAF2
-
- getTerminalVertices() - Method in class slib.graph.algo.extraction.rvf.RVF_DAG
-
Return the set of terminal vertices (leaves) reachable.
- getTraversalOrder() - Method in class slib.graph.algo.extraction.traversal.classical.DFS
-
Returns the traversal ordering resulting of the DFS i.e topological sort.
- getTraversalOrder() - Method in class slib.graph.algo.traversal.classical.DFS
-
Returns the traversal ordering resulting of the DFS i.e topological sort.
- getType() - Method in class slib.graph.io.loader.utils.filter.graph.Filter
-
- getType() - Method in class slib.sml.sm.core.measures.Dist_Pairwise
-
- getType() - Method in interface slib.sml.sm.core.measures.Measure
-
Specifies the type of measures.
- getType() - Method in class slib.sml.sm.core.measures.Sim_Groupwise
-
- getType() - Method in class slib.sml.sm.core.measures.Sim_Pairwise
-
- getType() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- getTypeUriString() - Method in class slib.graph.io.loader.bio.obo.utils.OboRelationship
-
- getUniqueTaxonomicRoot(G) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Return the unique vertex rooting the underlying taxonomic graph.
- getUniqueTaxonomicRoot(G) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Return the unique vertex rooting the underlying taxonomic graph.
- getUri() - Method in class slib.graph.io.conf.GraphConf
-
- getURI() - Method in interface slib.graph.model.graph.elements.E
-
- getURI() - Method in interface slib.graph.model.graph.G
-
- getURI() - Method in class slib.graph.model.impl.graph.elements.Edge
-
- getURI() - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getURI(String) - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- getURI(String, String) - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- getURI(String, boolean) - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- getURI(String) - Method in interface slib.graph.model.repo.URIFactory
-
- getURI(String, boolean) - Method in interface slib.graph.model.repo.URIFactory
-
- getURI(String, String) - Method in interface slib.graph.model.repo.URIFactory
-
- getURIPrefixes() - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- getURIPrefixes() - Method in interface slib.graph.model.repo.URIFactory
-
- getURIstring() - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- getURIstring() - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- getV(URI, WalkConstraint) - Method in interface slib.graph.model.graph.G
-
Retrieve view of all vertices of the graph which can be reached from a
given vertex respecting the given constraint.
- getV() - Method in interface slib.graph.model.graph.G
-
- getV(URI, URI, Direction) - Method in interface slib.graph.model.graph.G
-
Return all neighbors vertices of a given vertex considering a particular
direction and URI predicate.
- getV() - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getV(URI, URI, Direction) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getV(URI, WalkConstraint) - Method in class slib.graph.model.impl.graph.memory.GraphMemory
-
- getV_NoEdgeType(G, URI, Direction) - Static method in class slib.graph.algo.accessor.GraphAccessor
-
- getV_NoEdgeType(G, Set<URI>, Direction) - Static method in class slib.graph.algo.accessor.GraphAccessor
-
- getValue() - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- getValue(String) - Method in class slib.tools.module.GlobalConfPattern
-
- getValue() - Method in class slib.tools.ontofocus.core.utils.QueryEntryURI
-
- getValue(C, R) - Method in class slib.utils.impl.MatrixDouble
-
- getValue(Object, Object) - Method in class slib.utils.impl.MatrixDynamic
-
- getValue() - Method in class slib.utils.impl.QueryEntry
-
- getValue() - Method in class slib.utils.Pair
-
- getValueCheckIndex(C, R) - Method in class slib.utils.impl.MatrixDouble
-
- getVariables() - Method in class slib.tools.module.GlobalConfPattern
-
- getVector(Set<URI>, SMconf) - Method in class slib.sml.sm.core.engine.SM_Engine
-
- getVersion() - Method in class slib.tools.module.ModuleCst
-
- getVersionSnapshot() - Method in class slib.tools.module.ModuleCst
-
- getVMaxDepths() - Method in class slib.graph.algo.extraction.metric.DepthAnalyserAG
-
- getVMaxDepths() - Method in class slib.graph.algo.metric.DepthAnalyserAG
-
- getVMinDepths() - Method in class slib.graph.algo.extraction.metric.DepthAnalyserAG
-
- getVMinDepths() - Method in class slib.graph.algo.metric.DepthAnalyserAG
-
- getWalkConstraint() - Method in class slib.graph.algo.extraction.rvf.RVF
-
- getWeight(E) - Method in interface slib.graph.model.graph.weight.GWS
-
Access to the weight of the edge.
- getWeight(URI) - Method in interface slib.graph.model.graph.weight.GWS
-
Access to the weight defined for a specific predicate.
- getWeight(E) - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- getWeight(URI) - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- getWeightingScheme(String) - Method in class slib.sml.sm.core.engine.SM_Engine
-
TODO store the weighting scheme in a Map Provide a way to
load edge weight from file or to compute them using specific methods
- GFormat - Enum in slib.graph.io.util
-
- GlobalConfPattern - Class in slib.tools.module
-
- gmShortFlag - Variable in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- GO_BFS - Class in slib.examples.graph.traversal
-
Basic example which shows how to perform a Breadth-First Search on the Gene
Ontology.
- GO_BFS() - Constructor for class slib.examples.graph.traversal.GO_BFS
-
- GOID - Static variable in class slib.graph.io.loader.bio.gaf2.GraphLoader_GAF_2
-
- GRAPH_ATT - Static variable in class slib.tools.module.XmlTags
-
- GRAPH_ATTR - Static variable in class slib.tools.module.XmlTags
-
- GRAPH_RELATIONSHIP - Static variable in class slib.tools.module.XmlTags
-
- GRAPH_TAG - Static variable in class slib.tools.module.XmlTags
-
- GraphAccessor - Class in slib.graph.algo.accessor
-
- GraphAccessor() - Constructor for class slib.graph.algo.accessor.GraphAccessor
-
- GraphActionExecutor - Class in slib.graph.algo.extraction.utils
-
Class managing the execution of
GAction over a graph.
- GraphActionExecutor() - Constructor for class slib.graph.algo.extraction.utils.GraphActionExecutor
-
- GraphActionExecutor - Class in slib.graph.algo.utils
-
Class managing the execution of
GAction over a graph.
- GraphActionExecutor() - Constructor for class slib.graph.algo.utils.GraphActionExecutor
-
- GraphConf - Class in slib.graph.io.conf
-
- GraphConf() - Constructor for class slib.graph.io.conf.GraphConf
-
- GraphConf(URI) - Constructor for class slib.graph.io.conf.GraphConf
-
- GraphExample - Class in slib.examples.sml.general
-
Snippet of code showing how to interact with the graph, i.e.
- GraphExample() - Constructor for class slib.examples.sml.general.GraphExample
-
- GraphLoader - Interface in slib.graph.io.loader
-
Generic interface defining the methods a graph loader must implements
- GraphLoader_CSV - Class in slib.graph.io.loader.csv
-
- GraphLoader_CSV() - Constructor for class slib.graph.io.loader.csv.GraphLoader_CSV
-
- GraphLoader_GAF_2 - Class in slib.graph.io.loader.bio.gaf2
-
GAF 2 parser used to construct a graph from a GAF 2.0 annotation file
The parser consider considering GAF 2.0 specification provided at
http://wiki.geneontology.org/index.php/GO_Consortium_web_GAF2.0_documentation
http://www.geneontology.org/GO.format.gaf-2_0.shtml
TODO - Manage multiple organism specification : taxon:1|taxon:1000
- GraphLoader_GAF_2() - Constructor for class slib.graph.io.loader.bio.gaf2.GraphLoader_GAF_2
-
- GraphLoader_MESH_XML - Class in slib.graph.io.loader.bio.mesh
-
MeSH Loader.
- GraphLoader_MESH_XML() - Constructor for class slib.graph.io.loader.bio.mesh.GraphLoader_MESH_XML
-
- GraphLoader_OBO_1_2 - Class in slib.graph.io.loader.bio.obo
-
- GraphLoader_OBO_1_2() - Constructor for class slib.graph.io.loader.bio.obo.GraphLoader_OBO_1_2
-
- GraphLoader_SLIB - Class in slib.graph.io.loader.slibformat
-
TODO Comment DO not Support transitivity and inverse definitions anymore
- GraphLoader_SLIB() - Constructor for class slib.graph.io.loader.slibformat.GraphLoader_SLIB
-
- GraphLoader_TSVannot - Class in slib.graph.io.loader.annot
-
Class used to load annotation file:
XXXX1[TAB]c1;c2;c3
XXXX2[TAB]c2;c3
...
- GraphLoader_TSVannot() - Constructor for class slib.graph.io.loader.annot.GraphLoader_TSVannot
-
- GraphLoader_Wordnet - Class in slib.graph.io.loader.wordnet
-
- GraphLoader_Wordnet() - Constructor for class slib.graph.io.loader.wordnet.GraphLoader_Wordnet
-
- GraphLoaderGeneric - Class in slib.graph.io.loader
-
Graph Loader is a class used to facilitate graph loading.
- GraphLoaderGeneric() - Constructor for class slib.graph.io.loader.GraphLoaderGeneric
-
- GraphLoaderSnomedCT_RF2 - Class in slib.graph.io.loader.bio.snomedct
-
- GraphLoaderSnomedCT_RF2() - Constructor for class slib.graph.io.loader.bio.snomedct.GraphLoaderSnomedCT_RF2
-
- GraphMemory - Class in slib.graph.model.impl.graph.memory
-
In memory implementation of
G
- GraphMemory(URI) - Constructor for class slib.graph.model.impl.graph.memory.GraphMemory
-
Create a graph loaded in memory.
- GraphPlotter_Graphviz - Class in slib.graph.io.plotter
-
Class used to plot graph using Graphviz.
- GraphPlotter_Graphviz() - Constructor for class slib.graph.io.plotter.GraphPlotter_Graphviz
-
- GraphReduction_DAG_Ranwez_2011 - Class in slib.graph.algo.extraction.reduction.dag
-
Algorithm used to extract a subgraph from a DAG (Directed Acyclic Graph)
Implementation of Ranwez et al.
- GraphReduction_DAG_Ranwez_2011(G) - Constructor for class slib.graph.algo.extraction.reduction.dag.GraphReduction_DAG_Ranwez_2011
-
- GraphReduction_DAG_Ranwez_2011(G, Set<URI>, Set<URI>, boolean) - Constructor for class slib.graph.algo.extraction.reduction.dag.GraphReduction_DAG_Ranwez_2011
-
Method used to perform the subGraph extraction of an acyclic graph based
on top-down and bottom-up transitive closures.
- GraphReduction_DAG_Ranwez_2011 - Class in slib.graph.algo.reduction.dag
-
Algorithm used to extract a subgraph from a DAG (Directed Acyclic Graph)
Implementation of Ranwez et al.
- GraphReduction_DAG_Ranwez_2011(G) - Constructor for class slib.graph.algo.reduction.dag.GraphReduction_DAG_Ranwez_2011
-
- GraphReduction_DAG_Ranwez_2011(G, Set<URI>, Set<URI>, boolean) - Constructor for class slib.graph.algo.reduction.dag.GraphReduction_DAG_Ranwez_2011
-
Method used to perform the subGraph extraction of an acyclic graph based
on top-down and bottom-up transitive closures.
- GraphReduction_Transitive - Class in slib.graph.algo.extraction.reduction.dag
-
Class used to perform a transitive reduction of a DAG see
http://en.wikipedia.org/wiki/Transitive_reduction
- GraphReduction_Transitive() - Constructor for class slib.graph.algo.extraction.reduction.dag.GraphReduction_Transitive
-
- GraphReduction_Transitive - Class in slib.graph.algo.reduction.dag
-
Class used to perform a transitive reduction of a DAG see
http://en.wikipedia.org/wiki/Transitive_reduction
- GraphReduction_Transitive() - Constructor for class slib.graph.algo.reduction.dag.GraphReduction_Transitive
-
- GraphRepository - Interface in slib.graph.model.repo
-
Interface defining a repository for the graphs.
- GraphRepositoryMemory - Class in slib.graph.model.impl.repo
-
- GRAPHS_TAG - Static variable in class slib.tools.module.XmlTags
-
- GraphTraversal - Interface in slib.graph.algo.extraction.traversal
-
GraphTraversal interface
- GraphTraversal - Interface in slib.graph.algo.traversal
-
GraphTraversal interface
- graphURI - Variable in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- graphURI - Variable in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- GraphUtils - Class in slib.graph.model.impl.utils
-
- GraphUtils() - Constructor for class slib.graph.model.impl.utils.GraphUtils
-
- GROUPWISE_MEASURE_FLAGS - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- groupwiseClassName(String) - Static method in class slib.sml.sm.core.utils.SMConstants
-
Return the class Name of the given groupwise semantic measure flag
- groupwiseMeasureMapping - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- GWS - Interface in slib.graph.model.graph.weight
-
Object representing a Graph Weighting Scheme containing :
a default weight which is return each time a non specified weight is
queried (e.g.
- GWS_impl - Class in slib.graph.model.impl.graph.weight
-
In memory Graph Weighting Scheme (GWS) implementation of
GWS
- GWS_impl() - Constructor for class slib.graph.model.impl.graph.weight.GWS_impl
-
Create a weighting scheme with the default weight set to 1.
- GWS_impl(double) - Constructor for class slib.graph.model.impl.graph.weight.GWS_impl
-
Create a weighting scheme with a specific default weight.
- IC - Interface in slib.sml.sm.core.metrics.ic
-
Interface defining the methods representing an IC computer.
- ic - Variable in class slib.sml.sm.core.utils.OperatorConf
-
the IC configuration associated to the operator configuration.
- IC_annot_resnik_1995 - Class in slib.sml.sm.core.metrics.ic.annot
-
Implementation of the original definition of Information Content (IC)
proposed by Resnik.
- IC_annot_resnik_1995() - Constructor for class slib.sml.sm.core.metrics.ic.annot.IC_annot_resnik_1995
-
- IC_ANNOT_RESNIK_1995 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- IC_annot_resnik_1995_Normalized - Class in slib.sml.sm.core.metrics.ic.annot
-
ICi_resnik_1995
TODO Add resnik citation
p(c) defined as number of top down fashion path leading to c from the
reachable leaves from c + 1 max_pc = max p(c) for all concepts.
- IC_annot_resnik_1995_Normalized() - Constructor for class slib.sml.sm.core.metrics.ic.annot.IC_annot_resnik_1995_Normalized
-
- IC_ANNOT_RESNIK_1995_NORMALIZED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- IC_ATTR - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
- IC_ATTR_VALUE_FULL_LIST - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
Value to specify to compute measures using all loaded IC
- IC_Conf_Corpus - Class in slib.sml.sm.core.metrics.ic.utils
-
Class used to represent configurations dedicated to Corpus-based IC.
- IC_Conf_Corpus(String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Corpus
-
Build an instance of IC configuration.
- IC_Conf_Corpus(String, String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Corpus
-
Build an instance of IC configuration.
- IC_Conf_Corpus(String, String, String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Corpus
-
Build an instance of the configuration considering the given parameters.
- IC_Conf_Topo - Class in slib.sml.sm.core.metrics.ic.utils
-
- IC_Conf_Topo(String, String, String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Topo
-
- IC_Conf_Topo(String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Topo
-
- IC_Conf_Topo(String, String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.IC_Conf_Topo
-
Build an instance of IC configuration.
- IC_FLAGS - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- IC_PROB - Static variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Constants
-
- IC_PROB - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
- IC_PROB_OCCURENCE_PROPAGATED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- IC_probOccurence_propagatted - Class in slib.sml.sm.core.metrics.ic.annot
-
- IC_probOccurence_propagatted() - Constructor for class slib.sml.sm.core.metrics.ic.annot.IC_probOccurence_propagatted
-
- IC_SHORT_FLAG - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- IC_TAG - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
- ICconf - Class in slib.sml.sm.core.metrics.ic.utils
-
- ICconf(String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Builder of the IC configuration.
- ICconf(String, String, String) - Constructor for class slib.sml.sm.core.metrics.ic.utils.ICconf
-
Advanced builder of an instance of IC configuration.
- ICcorpus - Interface in slib.sml.sm.core.metrics.ic.annot
-
- ICi_ancestors_norm - Class in slib.sml.sm.core.metrics.ic.topo
-
Basic definition of an estimator of specificity based on the number of ancestors.
- ICi_ancestors_norm() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_ancestors_norm
-
- ICI_ANCESTORS_NORM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_depth_max_linear - Class in slib.sml.sm.core.metrics.ic.topo
-
- ICi_depth_max_linear() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_depth_max_linear
-
- ICI_DEPTH_MAX_LINEAR - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_depth_max_nonlinear - Class in slib.sml.sm.core.metrics.ic.topo
-
- ICi_depth_max_nonlinear() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_depth_max_nonlinear
-
- ICI_DEPTH_MAX_NONLINEAR - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_depth_min_nonlinear - Class in slib.sml.sm.core.metrics.ic.topo
-
- ICi_depth_min_nonlinear() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_depth_min_nonlinear
-
- ICI_DEPTH_MIN_NONLINEAR - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_harispe_2012 - Class in slib.sml.sm.core.metrics.ic.topo
-
Modification of Sanchez et al.
- ICi_harispe_2012() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_harispe_2012
-
- ICI_HARISPE_2012 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICI_PROB_OCCURENCE - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICI_PROB_OCCURENCE_PROPAGATED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_probOccurence - Class in slib.sml.sm.core.metrics.ic.topo
-
ICi_resnik_1995
TODO Add resnik citation
p(c) defined as number of top down fashion path leading to c from the
reachable leaves from c + 1 max_pc = max p(c) for all concepts.
- ICi_probOccurence() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_probOccurence
-
- ICi_probOccurence_propagatted - Class in slib.sml.sm.core.metrics.ic.topo
-
ICi_resnik_1995
TODO Add resnik citation
p(c) defined as number of top down fashion path leading to c from the
reachable leaves from c + 1 max_pc = max p(c) for all concepts.
- ICi_probOccurence_propagatted() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_probOccurence_propagatted
-
- ICi_resnik_1995 - Class in slib.sml.sm.core.metrics.ic.topo
-
ICi_resnik_1995
TODO Add resnik citation
p(c) defined as number of top down fashion path leading to c from the
reachable leaves from c + 1 max_pc = max p(c) for all concepts.
- ICi_resnik_1995() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_resnik_1995
-
- ICI_RESNIK_1995 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICI_RESNIK_UNPROPAGATED_1995 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_resnik_unpropagatted_1995 - Class in slib.sml.sm.core.metrics.ic.topo
-
ICi_resnik_1995
TODO Add resnik citation
p(c) defined as number of top down fashion path leading to c from the
reachable leaves from c + 1 max_pc = max p(c) for all concepts.
- ICi_resnik_unpropagatted_1995() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_resnik_unpropagatted_1995
-
- ICi_sanchez_2011 - Class in slib.sml.sm.core.metrics.ic.topo
-
Reference: Sanchez D, Batet M, Isern D: Ontology-based information content
computation.
- ICi_sanchez_2011() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_sanchez_2011
-
- ICI_SANCHEZ_2011 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_sanchez_2011_b_adapted - Class in slib.sml.sm.core.metrics.ic.topo
-
Reference: Sanchez D, Batet M, Isern D: Ontology-based information content
computation.
- ICi_sanchez_2011_b_adapted() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_sanchez_2011_b_adapted
-
- ICI_SANCHEZ_2011_b_adapted - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_seco_2004 - Class in slib.sml.sm.core.metrics.ic.topo
-
Seco N, Veale T, Hayes J: An Intrinsic Information Content Metric for
Semantic Similarity in WordNet.
- ICi_seco_2004() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_seco_2004
-
- ICI_SECO_2004 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICi_zhou_2008 - Class in slib.sml.sm.core.metrics.ic.topo
-
Zhou Z, Wang Y, Gu J: A New Model of Information Content for Semantic
Similarity in WordNet.
- ICi_zhou_2008() - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_zhou_2008
-
Builder of an instance of IC computer.
- ICi_zhou_2008(double) - Constructor for class slib.sml.sm.core.metrics.ic.topo.ICi_zhou_2008
-
Builder of an instance of IC computer.
- ICI_ZHOU_2008 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICS_TAG - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
- icShortFlag - Variable in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- icsMapping - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- ICtopo - Interface in slib.sml.sm.core.metrics.ic.topo
-
Class representing Topological Information Content
- IcUtils - Class in slib.sml.sm.core.metrics.ic.utils
-
Class used to defined static methods utility.
- IcUtils() - Constructor for class slib.sml.sm.core.metrics.ic.utils.IcUtils
-
- id - Variable in class slib.sml.sm.core.utils.OperatorConf
-
the unique id identifying the configuration.
- ID_ATTR - Static variable in class slib.tools.module.XmlTags
-
- ID_SUBCLASSOF_SNOMED - Static variable in class slib.graph.io.loader.bio.snomedct.GraphLoaderSnomedCT_RF2
-
- IDist_Pairwise - Interface in slib.sml.sm.core.measures
-
Interface used to represent a pairwise measure which can be used to compute
the semantic similarity of a pair of concepts/classes.
- IDist_Pairwise_DAG - Interface in slib.sml.sm.core.measures.graph.pairwise.dag
-
Interface of a semantic similarity measure which can be used to compute the
semantic similarity of two classes/concepts structured in a Directed Acyclic
Graph (DAG).
- idMapping - Static variable in class slib.graph.io.loader.bio.snomedct.GraphLoaderSnomedCT_RF2
-
- incR - Variable in class slib.tools.ontofocus.cli.OntoFocusCmdHandler
-
- incR - Static variable in class slib.tools.ontofocus.cli.utils.OntoFocusCmdHandlerCst
-
- incR_Separator - Static variable in class slib.tools.ontofocus.cli.utils.OntoFocusCmdHandlerCst
-
separator used to defined multiple relationships to consider during the process
- Indexer_MESH_XML - Class in slib.indexer.mesh
-
Class used to build an index for the descriptors specified in the MeSH XML.
- Indexer_MESH_XML() - Constructor for class slib.indexer.mesh.Indexer_MESH_XML
-
- IndexerOBO - Class in slib.indexer.obo
-
Class used to build an index for the terms specified in an OBO ontology
- IndexerOBO() - Constructor for class slib.indexer.obo.IndexerOBO
-
- IndexerSNOMEDCT_RF2 - Class in slib.indexer.snomed_ct
-
- IndexerSNOMEDCT_RF2() - Constructor for class slib.indexer.snomed_ct.IndexerSNOMEDCT_RF2
-
- IndexerWordNetBasic - Class in slib.indexer.wordnet
-
DUMMY INDEXER USED TO DEBUG.
- IndexerWordNetBasic() - Constructor for class slib.indexer.wordnet.IndexerWordNetBasic
-
- IndexerWordNetBasic(URIFactory, G, String) - Constructor for class slib.indexer.wordnet.IndexerWordNetBasic
-
- IndexHash - Class in slib.indexer
-
Class used to associate an URI to an object which contains its descriptions
as String values.
- IndexHash() - Constructor for class slib.indexer.IndexHash
-
- InstanceAccessor_RDF_TYPE - Class in slib.graph.algo.extraction.rvf.instances.impl
-
- InstanceAccessor_RDF_TYPE(G, DescendantEngine) - Constructor for class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- InstanceAccessor_RDF_TYPE(G) - Constructor for class slib.graph.algo.extraction.rvf.instances.impl.InstanceAccessor_RDF_TYPE
-
- InstancesAccessor - Interface in slib.graph.algo.extraction.rvf.instances
-
Interface defining a access to the instances of the classes
- intersection(Collection<X>, Collection<X>) - Static method in class slib.utils.impl.SetUtils
-
Compute the intersection of two collections
- IO_RuntimeException - Exception in slib.utils.impl
-
TODO modify or remove
- IO_RuntimeException(String) - Constructor for exception slib.utils.impl.IO_RuntimeException
-
- IS_SYMMETRIC - Static variable in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Lin_1998
-
- ISA_FLAG - Static variable in class slib.utils.impl.OBOconstants
-
- isAllow_all_gafVersion() - Method in class slib.graph.io.loader.bio.obo.GraphLoader_OBO_1_2
-
- isCachePairwiseResults() - Method in class slib.sml.sm.core.engine.SM_Engine
-
Check if the engine is configured to store the results of the pairwise
semantic measure computation.
- isCorpusBased() - Method in class slib.sml.sm.core.metrics.ic.utils.ICconf
-
- isDag(G, Set<URI>, WalkConstraint) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
- isDag(G, URI, WalkConstraint) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Check if the underlying graph defined by the edges of the given edge
types and build using a traversal starting from the given root node is a
DAG.
- isDag(G, WalkConstraint) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Check if the underlying graph defined by given
WalkConstraint is
a DAG.
- isDag(G, Set<URI>, WalkConstraint) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
- isDag(G, URI, WalkConstraint) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Check if the underlying graph defined by the edges of the given edge
types and build using a traversal starting from the given root node is a
DAG.
- isDag(G, WalkConstraint) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Check if the underlying graph defined by given
WalkConstraint is
a DAG.
- isGraphRegistred(URI) - Method in class slib.graph.model.impl.repo.GraphRepositoryMemory
-
- isGraphRegistred(URI) - Method in interface slib.graph.model.repo.GraphRepository
-
Check if a graph is registred to the given URI.
- ISim_Pairwise - Interface in slib.sml.sm.core.measures
-
Interface used to represent a pairwise measure which can be used to compute
the semantic similarity of a pair of concepts/classes.
- ISim_Pairwise_DAG - Interface in slib.sml.sm.core.measures.graph.pairwise.dag
-
Interface of a semantic similarity measure which can be used to compute the
semantic similarity of two classes/concepts structured in a Directed Acyclic
Graph (DAG).
- isInColumnIndex(C) - Method in class slib.utils.impl.MatrixDouble
-
- isInColumnIndex(Object) - Method in class slib.utils.impl.MatrixDynamic
-
- isInIndexed(Object) - Method in class slib.utils.impl.MatrixDynamic
-
- isInRowIndex(R) - Method in class slib.utils.impl.MatrixDouble
-
- isInRowIndex(Object) - Method in class slib.utils.impl.MatrixDynamic
-
- isNormalized() - Method in class slib.sml.sm.core.measures.Dist_Pairwise
-
- isNormalized() - Method in interface slib.sml.sm.core.measures.Measure
-
Specified if the measure is normalized.
- isNormalized() - Method in class slib.sml.sm.core.measures.Sim_Groupwise
-
- isNormalized() - Method in class slib.sml.sm.core.measures.Sim_Pairwise
-
- isObsolete() - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- isObsolete() - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- isOutputBaseName() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- isQuiet() - Method in class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- isRemoveEmpty() - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- ISSchildren - Static variable in class slib.graph.io.loader.bio.gaf2.EvidenceCodeRules
-
- isSquare() - Method in class slib.utils.impl.MatrixDouble
-
- isSquare() - Method in class slib.utils.impl.MatrixDynamic
-
- isSymmetric() - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.Dist_Pairwise
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Batet_2010
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Braun_Blanquet_1932
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Dice_1945
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Jaccard_1901
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Knappe_2004
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Korbel_2002
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Maryland_Bridge_2003
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Ochiai_1957
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Simpson_1960
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Sokal_Sneath_1963
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Tversky_1977
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Dist_pairwise_DAG_edge_Rada_1989
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Dist_pairwise_DAG_edge_Rada_LCA_1989
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Leacock_Chodorow_1998
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Pekar_Staab_2002
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_1989
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_LCA_1989
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Stojanovic_2001
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Wu_Palmer_1994
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_GL
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_3W_IC
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_IC
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Lin_1998
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Resnik_1995
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Schlicker_2006_SimRel
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Sim_IC_2010
-
- isSymmetric() - Method in interface slib.sml.sm.core.measures.Measure
-
Specified if the measure is symmetric.
- isSymmetric() - Method in class slib.sml.sm.core.measures.others.pairwise.Sim_pairwise_Random
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.Sim_Groupwise
-
- isSymmetric() - Method in class slib.sml.sm.core.measures.Sim_Pairwise
-
- isTransitive() - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- isUniqueRootedDagRoot(G, URI, WalkConstraint) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
Do not check if the graph is a DAG
- isUniqueRootedDagRoot(G, URI, WalkConstraint) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
Do not check if the graph is a DAG
- isUniqueRootedTaxonomicDag(G, URI) - Method in class slib.graph.algo.extraction.validator.dag.ValidatorDAG
-
- isUniqueRootedTaxonomicDag(G, URI) - Method in class slib.graph.algo.validator.dag.ValidatorDAG
-
- isUseLoadedURIprefixes() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- isUseLoadedURIprefixesOutput() - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- isValid() - Method in class slib.graph.algo.extraction.utils.GAction
-
Check if the action is valid with regards to the parameters required to be specified.
- isValid() - Method in class slib.graph.algo.utils.GAction
-
Check if the action is valid with regards to the parameters required to be specified.
- isValid() - Method in class slib.graph.io.conf.GDataConf
-
- isValid() - Method in class slib.graph.io.conf.GraphConf
-
- isValid() - Method in interface slib.tools.module.ModuleConf
-
Check if the current configuration is valid i.e.
- isValid() - Method in class slib.tools.ontofocus.core.utils.QueryEntryURI
-
Only check if K and V are defined
anf if their are not equals to empty string / Set
- isValid() - Method in interface slib.utils.i.CheckableValidity
-
- isValid() - Method in class slib.utils.impl.QueryEntry
-
Only check if K and V are defined anf if their are not equals to empty
string
- searchMax_IC_MICA(URI, URI, Set<URI>, Set<URI>, Map<URI, Double>) - Static method in class slib.sml.sm.core.metrics.ic.utils.IcUtils
-
Search the IC of Most Informative Concept Shared between two sets,
regarding the given metric.
- searchMICA(URI, URI, Set<URI>, Set<URI>, Map<URI, Double>) - Static method in class slib.sml.sm.core.metrics.ic.utils.IcUtils
-
Search the Most Informative Concept Shared between two sets, regarding
the given metric.
- searchMin_pOc_MICA(Set<URI>, Set<URI>, Map<URI, Double>) - Static method in class slib.sml.sm.core.metrics.ic.utils.IcUtils
-
Search the IC of Less Informative Concept Shared between two sets,
regarding the given metric.
- searchMSA(Set<URI>, Map<URI, Integer>) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils.SimDagEdgeUtils
-
Search the Most specific ancestor considering the depth
- semanticMeasureClassName(String) - Static method in class slib.sml.sm.core.utils.SMConstants
-
Return the class Name of the given semantic measure flag
- setActions(List<GAction>) - Method in class slib.graph.io.conf.GraphConf
-
- setAllow_all_gafVersion(boolean) - Method in class slib.graph.io.loader.bio.obo.GraphLoader_OBO_1_2
-
- setAnnotsFormat(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setAnnotsPath(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setAspect(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setBATCH_LIMIT(int) - Method in class slib.sml.smutils.SQLiteUtils
-
Setter of the number of value stored in memory.
- setBATCH_LIMIT_MATRIX_LINE(int) - Method in class slib.sml.smutils.SQLiteUtils
-
Mutator of the number of values stored by line.
- setCachePairwiseResults(boolean) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Set the configuration of the engine regarding pairwise semantic measure
score caching.
- setData(List<GDataConf>) - Method in class slib.graph.io.conf.GraphConf
-
- setDefaultWeight(double) - Method in interface slib.graph.model.graph.weight.GWS
-
Set the weight defined by default
- setDefaultWeight(double) - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- setDescriptorName(String) - Method in class slib.graph.io.loader.bio.mesh.MeshConcept
-
- setDescriptorName(String) - Method in class slib.indexer.mesh.MeshDescriptor
-
- setDescriptorUI(String) - Method in class slib.graph.io.loader.bio.mesh.MeshConcept
-
- setDescriptorUI(String) - Method in class slib.indexer.mesh.MeshDescriptor
-
- setDocFields(Collection<String>) - Method in class slib.sml.sm.core.measures.corpus.VocContextMatrixBuilder
-
- setFilter(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setFormat(GFormat) - Method in class slib.graph.io.conf.GDataConf
-
- setGmShortFlag(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setGraphURI(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setICconf(ICconf) - Method in class slib.sml.sm.core.utils.SMconf
-
Mutator of the IC configuration.
- setIcShortFlag(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setICSvalues(ICconf, Map<URI, Double>) - Method in class slib.sml.sm.core.engine.SM_Engine
-
Set the ICS stored for the given IC configuration to the specified set of
values.
- setId(String) - Method in class slib.graph.io.loader.utils.filter.graph.Filter
-
- setInfile(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setJobSize(int) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- setK(double) - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Knappe_2004
-
- setK(double) - Method in class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Tversky_1977
-
Setter of the k parameter value
- setLabel(String) - Method in class slib.sml.sm.core.utils.SMconf
-
- setLoc(String) - Method in class slib.graph.io.conf.GDataConf
-
- setLogBase(Double) - Method in class slib.sml.sm.core.metrics.utils.LogBasedMetric
-
- setLogBase(Conf) - Method in class slib.sml.sm.core.metrics.utils.LogBasedMetric
-
- setLogBase(Double) - Method in interface slib.sml.sm.core.metrics.utils.LogBasedMetricInterface
-
Mutator of the log base associated to the metric.
- setLogBase(Conf) - Method in interface slib.sml.sm.core.metrics.utils.LogBasedMetricInterface
-
Mutator of the log base associated to the metric.
- setMaxThread(int) - Method in class slib.utils.threads.ThreadManager
-
- setMetric(String) - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- setMtype(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setNoAnnotAction(ActionsParams) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setNoAnnotationScore(double) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setNoAnnots(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setNoFoundAction(ActionsParams) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setNoFoundScore(double) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setNotFound(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setNoTR_Annots(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setNoTR_KR(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setObsolete(boolean) - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- setObsolete(boolean) - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- setOntologyFormat(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setOntologyPath(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setOutfile(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setOutput(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setOutputBaseName(boolean) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setParams(HashMap<String, Object>) - Method in class slib.utils.i.Conf
-
Set the current map to the given.
- setPmShortFlag(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setPreferredDescription(String) - Method in interface slib.indexer.URIDescription
-
Set the preferred description of the resource.
- setPreferredDescription(String) - Method in class slib.indexer.URIDescriptionBasic
-
- setPrefixURIAttribut(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setPreventIncoherency(boolean) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Lin_1998
-
Setting this parameter you can decide if incoherences in the input
parameters must be detected (true) or not (false) - default true.
- setProperty(String, Object) - Method in class slib.utils.impl.OProperty
-
- setQueries(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setQuiet(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setRelationships(ArrayList<OboRelationship>) - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- setRemoveEmpty(boolean) - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- setSetValue(int) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- setSkipped(int) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.calc.ThreadResultsQueryLoader
-
- setSymmetricity(boolean) - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- setTargetUriString(String) - Method in class slib.graph.io.loader.bio.obo.utils.OboRelationship
-
- setThreads(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
-
- setTransitivity(boolean) - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- setType(String) - Method in class slib.graph.io.loader.utils.filter.graph.Filter
-
- setType(String) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setTypeUriString(String) - Method in class slib.graph.io.loader.bio.obo.utils.OboRelationship
-
- setUri(URI) - Method in class slib.graph.io.conf.GraphConf
-
- setURIstring(String) - Method in class slib.graph.io.loader.bio.obo.utils.OboTerm
-
- setURIstring(String) - Method in class slib.graph.io.loader.bio.obo.utils.OboType
-
- setUseLoadedURIprefixes(boolean) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- setUseLoadedURIprefixesOutput(boolean) - Method in class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
-
- SetUtils - Class in slib.utils.impl
-
- SetUtils() - Constructor for class slib.utils.impl.SetUtils
-
- setValue(double) - Method in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics
-
- setValue(Set<URI>) - Method in class slib.tools.ontofocus.core.utils.QueryEntryURI
-
- setValue(C, R, Double) - Method in class slib.utils.impl.MatrixDouble
-
- setValue(Object, Object, N) - Method in class slib.utils.impl.MatrixDynamic
-
- setValue(String) - Method in class slib.utils.impl.QueryEntry
-
- setWalkConstraint(WalkConstraint) - Method in class slib.graph.algo.extraction.rvf.RVF
-
- setWeight(E, double) - Method in interface slib.graph.model.graph.weight.GWS
-
Set the weight for an edge
- setWeight(URI, double) - Method in interface slib.graph.model.graph.weight.GWS
-
Set the default weight for the specified URI.
- setWeight(E, double) - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- setWeight(URI, double) - Method in class slib.graph.model.impl.graph.weight.GWS_impl
-
- SHORT_FLAG_PM_SCHLICKER - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- shortestPath(URI, URI) - Method in class slib.graph.algo.extraction.shortest_path.Dijkstra
-
Compute shortest path between two nodes Note also that the resultStack is
populated during computation
- shortestPath(URI) - Method in class slib.graph.algo.extraction.shortest_path.Dijkstra
-
- shortestPath(URI, URI) - Method in class slib.graph.algo.shortest_path.Dijkstra
-
Compute shortest path between two nodes Note also that the resultStack is
populated during computation
- shortestPath(URI) - Method in class slib.graph.algo.shortest_path.Dijkstra
-
- shortURIasString(URI) - Method in class slib.graph.model.impl.repo.URIFactoryMemory
-
- shortURIasString(URI) - Method in interface slib.graph.model.repo.URIFactory
-
Create a string representing the URI using the loaded prefixes if any can be used
- showCmdLineExamples() - Method in class slib.tools.module.CmdHandler
-
- showContact() - Method in class slib.tools.module.CmdHandler
-
- showDescription() - Method in class slib.tools.module.CmdHandler
-
Show the description of the module if any
- showRef() - Method in class slib.tools.module.CmdHandler
-
- shutdown() - Method in class slib.utils.threads.PoolWorker
-
- shutdown(long, TimeUnit) - Method in class slib.utils.threads.PoolWorker
-
- sim(URI, URI, Set<URI>, Set<URI>, Map<URI, Double>, Map<URI, Double>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_G_SESAME_2007
-
- sim(double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_Resnik_1995
-
- sim(URI, URI, Set<URI>, Set<URI>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_Slimani_2006
-
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Kyogoku_basic_2011
-
Compute the semantic similarity considering the given parameters.
- sim(Double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Leacock_Chodorow_1998
-
Compute the semantic similarity considering the given parameters.
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Pekar_Staab_2002
-
Compute the semantic similarity considering the given parameters.
- sim(double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_1989
-
Compute the Rada similarity given the distance of the shortest path
linking the two concepts.
- sim(Map<URI, Double>, Map<URI, Double>, Set<URI>, Set<URI>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_LCA_1989
-
Compute RADA based semantic similarity.
- sim(URI, URI, Collection<URI>, Collection<URI>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Stojanovic_2001
-
Compute the semantic similarity considering the specified parameters.
- sim(URI, URI, Set<URI>, Set<URI>, Map<URI, Double>, Map<URI, Double>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Wu_Palmer_1994
-
compute the semantic similarity considering the given parameters.
- sim(double, Set<URI>, Set<URI>, Map<URI, Integer>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental.Sim_pairwise_DAG_edge_Li_2003
-
Revenir sur la recherche du msa de Li Pour Li le msa est le concept de
plus faible profondeur qui appartient au chemin le plus court entre les
deux concepts passant par un ancetre commun des deux concepts
Alpha in [0,1] (best : 0.2) Beta in ]0,1] (best : 0.6)
- sim(Set<URI>, Set<URI>, Set<URI>) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental.Sim_pairwise_DAG_hybrid_Ranwez_2006
-
- sim(double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_GL_GraSM
-
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Lin_1998_GraSM
-
- sim(double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Resnik_1995_GraSM
-
- sim(double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel
-
- sim(double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel
-
- sim(double, double, double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel
-
- sim(double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_GL
-
- sim(double, double, double, double, double, double) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
- sim(double, double, double, double, double) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model
-
- sim(double, double, double, double, double, double) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
- sim(double, double, double, double, double) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model
-
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_3W_IC
-
Compute the semantic similarity considering the given parameters.
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_IC
-
Compute the semantic similarity considering the given parameters.
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997
-
Compute the semantic similarity considering the given parameters.
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm
-
Compute the semantic similarity considering the given parameters.
- sim(double, double, double) - Static method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Lin_1998
-
Compute the similarity considering the given information content values.
- sim(double, double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Schlicker_2006_SimRel
-
Compute the semantic similarity considering the given parameters
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Sim_IC_2010
-
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_AVERAGE_NORMALIZED_GOSIM
-
- sim(double, double, double) - Method in class slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_MAX_NORMALIZED_GOSIM
-
See Sim_groupwise_Max to compute max values
- sim(MatrixDouble<URI, URI>) - Static method in class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Average
-
Compute the average of the values stored in the given matrix.
- sim(MatrixDouble<URI, URI>) - Static method in class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_BestMatchAverage
-
- sim(MatrixDouble<URI, URI>) - Static method in class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_BestMatchMax
-
- sim(MatrixDouble<URI, URI>) - Static method in class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Max
-
- sim(MatrixDouble<URI, URI>) - Static method in class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Min
-
- sim(String, String) - Method in class slib.sml.sm.core.measures.string.LevenshteinSimilarity
-
- sim(double[], double[]) - Static method in class slib.sml.sm.core.measures.vector.CosineSimilarity
-
Compute the cosine similarity of two vectors of the same length
- Sim_DAG_edge_abstract - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Class used to represent a
Sim_Pairwise_DAG which relies on a
edge-based approach.
- Sim_DAG_edge_abstract() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_DAG_edge_abstract
-
- Sim_DAG_hybrid_abstract - Class in slib.sml.sm.core.measures.graph.pairwise.dag.hybrid
-
Class used to represent a semantic similarity measure which is based on a
hybrid approach.
- Sim_DAG_hybrid_abstract() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.Sim_DAG_hybrid_abstract
-
- Sim_DAG_node_abstract - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
- Sim_DAG_node_abstract() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_DAG_node_abstract
-
- Sim_Framework_DAG_Set_abstract - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Abstract class used to facilitate implementation of set based measures.
- Sim_Framework_DAG_Set_abstract() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_abstract
-
- Sim_Framework_DAG_Set_Bader_2003 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Bader G, Hogue C: An automated method for finding molecular complexes in
large protein interaction networks.
- Sim_Framework_DAG_Set_Bader_2003() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Bader_2003
-
- SIM_FRAMEWORK_DAG_SET_BADER_2003 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_FRAMEWORK_DAG_SET_BASED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Batet_2010 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Batet M, Sanchez D, Valls A: An ontology-based measure to compute semantic
similarity in biomedicine.
- Sim_Framework_DAG_Set_Batet_2010() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Batet_2010
-
- SIM_FRAMEWORK_DAG_SET_BATET_2010 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Braun_Blanquet_1932 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Braun-Blanquet J: Plant sociology: the study of plant communities.
- Sim_Framework_DAG_Set_Braun_Blanquet_1932() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Braun_Blanquet_1932
-
- SIM_FRAMEWORK_DAG_SET_BRAUN_BLANQUET_1932 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Dice_1945 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Dice LR: Measures of the Amount of Ecologic Association Between Species.
- Sim_Framework_DAG_Set_Dice_1945() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Dice_1945
-
- SIM_FRAMEWORK_DAG_SET_DICE_1945 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Jaccard_1901 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Jaccard P: Distribution de la flore alpine dans le bassin des Dranses et dans
quelques regions voisines.
- Sim_Framework_DAG_Set_Jaccard_1901() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Jaccard_1901
-
- SIM_FRAMEWORK_DAG_SET_JACCARD_1901 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Knappe_2004 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Knappe R, Bulskov H, Andreasen T: Perspectives on ontology-based
querying.
- Sim_Framework_DAG_Set_Knappe_2004() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Knappe_2004
-
- Sim_Framework_DAG_Set_Knappe_2004(double) - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Knappe_2004
-
- SIM_FRAMEWORK_DAG_SET_KNAPPE_2004 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Korbel_2002 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Korbel JO, Snel B, Huynen M a, Bork P: SHOT: a web server for the
construction of genome phylogenies.
- Sim_Framework_DAG_Set_Korbel_2002() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Korbel_2002
-
- SIM_FRAMEWORK_DAG_SET_KORBEL_2002 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Maryland_Bridge_2003 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Mirkin B, Koonin E: A top-down method for building genome classification
trees with linear binary hierarchies.
- Sim_Framework_DAG_Set_Maryland_Bridge_2003() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Maryland_Bridge_2003
-
- SIM_FRAMEWORK_DAG_SET_MARYLAND_BRIDGE_2003 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Ochiai_1957 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Ochiai A: Zoogeographic studies on the soleoid fishes found in Japan and
its neighbouring regions.
- Sim_Framework_DAG_Set_Ochiai_1957() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Ochiai_1957
-
- SIM_FRAMEWORK_DAG_SET_OCHIAI_1957 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Simpson_1960 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Simpson GG: Notes on the measurement of faunal resemblance.
- Sim_Framework_DAG_Set_Simpson_1960() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Simpson_1960
-
- SIM_FRAMEWORK_DAG_SET_SIMPSON_1960 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Sokal_Sneath_1963 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Sokal RR, Sneath PHA: Principles of numerical taxonomy.
- Sim_Framework_DAG_Set_Sokal_Sneath_1963() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Sokal_Sneath_1963
-
- SIM_FRAMEWORK_DAG_SET_SOKAL_SNEATH_1963 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Framework_DAG_Set_Tversky_1977 - Class in slib.sml.sm.core.measures.graph.framework.dag
-
Tversky A: Features of similarity.
- Sim_Framework_DAG_Set_Tversky_1977() - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Tversky_1977
-
Create a Tversky Contrast Model semantic similarity instance with k
parameter equals to 0.5
- Sim_Framework_DAG_Set_Tversky_1977(double) - Constructor for class slib.sml.sm.core.measures.graph.framework.dag.Sim_Framework_DAG_Set_Tversky_1977
-
Create a Tversky Contrast Model semantic similarity instance.
- SIM_FRAMEWORK_DAG_SET_TVERSKY_1977 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Groupwise - Class in slib.sml.sm.core.measures
-
Interface used to represent Semantic similarity used to process pairs of groups of vertices.
- Sim_Groupwise() - Constructor for class slib.sml.sm.core.measures.Sim_Groupwise
-
- SIM_GROUPWISE_ADD_ON - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_Average - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
Classic Average Measure Assumes score symmetry
- Sim_groupwise_Average() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Average
-
- SIM_GROUPWISE_AVERAGE - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_AVERAGE_NORMALIZED_GOSIM - Class in slib.sml.sm.core.measures.others.groupwise.indirect.experimental
-

Frohlich H, Speer N, Poustka A, Beissbarth T: GOSim--an R-package for
computation of information theoretic GO similarities between terms and gene
products.
- Sim_groupwise_AVERAGE_NORMALIZED_GOSIM() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_AVERAGE_NORMALIZED_GOSIM
-
- SIM_GROUPWISE_AVERAGE_NORMALIZED_GOSIM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_GROUPWISE_BEST_MATCH_AVERAGE - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_GROUPWISE_BEST_MATCH_MAX - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_BestMatchAverage - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
Schlicker A, Domingues FS, Rahnenführer J, Lengauer T: A new measure for
functional similarity of gene products based on Gene Ontology.
- Sim_groupwise_BestMatchAverage() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_BestMatchAverage
-
- Sim_groupwise_BestMatchMax - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
Schlicker A, Domingues FS, Rahnenführer J, Lengauer T: A new measure for
functional similarity of gene products based on Gene Ontology.
- Sim_groupwise_BestMatchMax() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_BestMatchMax
-
- SIM_GROUPWISE_DAG - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_abstract - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Abstract class used to represent a semantic measure which can be applied
between two sets of concepts expressed in a Directed Acyclic Graph (DAG).
- Sim_groupwise_DAG_abstract() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_abstract
-
- Sim_groupwise_DAG_Ali_Deane - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Ali W, Deane CM.
- Sim_groupwise_DAG_Ali_Deane() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_Ali_Deane
-
- SIM_GROUPWISE_DAG_ALI_DEANE - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_GIC - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Pesquita C, Faria D, Bastos H: Evaluating gobased semantic similarity
measures.
- Sim_groupwise_DAG_GIC() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_GIC
-
- SIM_GROUPWISE_DAG_GIC - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_Lee_2004 - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P: Coexpression analysis of human
genes across many microarray data sets.
- Sim_groupwise_DAG_Lee_2004() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_Lee_2004
-
- SIM_GROUPWISE_DAG_LEE_2004 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_LP - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Gentleman R: Visualizing and distances using GO.
- Sim_groupwise_DAG_LP() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_LP
-
- SIM_GROUPWISE_DAG_LP - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_NTO - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Mistry M, Pavlidis P: Gene Ontology term overlap as a measure of gene
functional similarity.
- Sim_groupwise_DAG_NTO() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_NTO
-
- SIM_GROUPWISE_DAG_NTO - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_NTO_MAX - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Adaptation of Mistry M, Pavlidis P: Gene Ontology term overlap as a measure
of gene functional similarity.
- Sim_groupwise_DAG_NTO_MAX() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_NTO_MAX
-
- SIM_GROUPWISE_DAG_NTO_MAX - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_TO - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Mistry M, Pavlidis P: Gene Ontology term overlap as a measure of gene
functional similarity.
- Sim_groupwise_DAG_TO() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_TO
-
- SIM_GROUPWISE_DAG_TO - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_DAG_UI - Class in slib.sml.sm.core.measures.graph.groupwise.dag
-
Gentleman R: Visualizing and distances using GO.
- Sim_groupwise_DAG_UI() - Constructor for class slib.sml.sm.core.measures.graph.groupwise.dag.Sim_groupwise_DAG_UI
-
- SIM_GROUPWISE_DAG_UI - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Groupwise_Direct - Class in slib.sml.sm.core.measures
-
Interface used to represent direct groupwise measures.
- Sim_Groupwise_Direct() - Constructor for class slib.sml.sm.core.measures.Sim_Groupwise_Direct
-
- Sim_Groupwise_Indirect - Class in slib.sml.sm.core.measures
-
Interface used to represent groupwise measures based on a pairwise measures.
- Sim_Groupwise_Indirect() - Constructor for class slib.sml.sm.core.measures.Sim_Groupwise_Indirect
-
- Sim_groupwise_Lord_2003 - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
Lord P: Investigating semantic similarity measures across the Gene Ontology:
the relationship between sequence and annotation.
- Sim_groupwise_Lord_2003() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Lord_2003
-
- Sim_groupwise_Max - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
- Sim_groupwise_Max() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Max
-
- SIM_GROUPWISE_MAX - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_MAX_NORMALIZED_GOSIM - Class in slib.sml.sm.core.measures.others.groupwise.indirect.experimental
-

Frohlich H, Speer N, Poustka A, Beissbarth T: GOSim--an R-package for
computation of information theoretic GO similarities between terms and gene
products.
- Sim_groupwise_MAX_NORMALIZED_GOSIM() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_MAX_NORMALIZED_GOSIM
-
- SIM_GROUPWISE_MAX_NORMALIZED_GOSIM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_Min - Class in slib.sml.sm.core.measures.others.groupwise.indirect
-
- Sim_groupwise_Min() - Constructor for class slib.sml.sm.core.measures.others.groupwise.indirect.Sim_groupwise_Min
-
- SIM_GROUPWISE_MIN - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_GROUPWISE_OTHERS - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_groupwise_Random - Class in slib.sml.sm.core.measures.others.groupwise.direct
-
Random measure (used for test)
- Sim_groupwise_Random() - Constructor for class slib.sml.sm.core.measures.others.groupwise.direct.Sim_groupwise_Random
-
- SIM_GROUPWISE_RANDOM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_GROUPWISE_SHORT_FLAG - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_GROUPWISE_SVM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_Pairwise - Class in slib.sml.sm.core.measures
-
Interface used to represent a pairwise measure which can be used to compute
the semantic similarity of a pair of concepts/classes.
- Sim_Pairwise() - Constructor for class slib.sml.sm.core.measures.Sim_Pairwise
-
- Sim_Pairwise_DAG - Class in slib.sml.sm.core.measures.graph.pairwise.dag
-
- Sim_Pairwise_DAG() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.Sim_Pairwise_DAG
-
- Sim_pairwise_DAG_edge_Al_Mubaid_2006 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental
-
Al-Mubaid H, Nguyen HA: A cluster-based approach for semantic similarity in
the biomedical domain.
- Sim_pairwise_DAG_edge_Al_Mubaid_2006() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_Al_Mubaid_2006
-
- SIM_PAIRWISE_DAG_EDGE_BASED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_G_SESAME_2007 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental
-
TODO Check approximation using depth of concepts
- Sim_pairwise_DAG_edge_G_SESAME_2007() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_G_SESAME_2007
-
- Sim_pairwise_DAG_edge_Kyogoku_basic_2011 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Kyogoku R, Fujimoto R, Ozaki T, Ohkawa T: A method for supporting retrieval
of articles on protein structure analysis considering users ’ intention.
- Sim_pairwise_DAG_edge_Kyogoku_basic_2011() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Kyogoku_basic_2011
-
- SIM_PAIRWISE_DAG_EDGE_KYOGOKU_BASIC_2011 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Leacock_Chodorow_1998 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Implementation of Leacock and Chodorow semantic similarity measure.
- Sim_pairwise_DAG_edge_Leacock_Chodorow_1998() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Leacock_Chodorow_1998
-
- SIM_PAIRWISE_DAG_EDGE_LEACOCK_CHODOROW_1998 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Li_2003 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental
-
Li Y, Bandar ZA, McLean D: An approach for measuring semantic similarity
between words using multiple information sources.
- Sim_pairwise_DAG_edge_Li_2003() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental.Sim_pairwise_DAG_edge_Li_2003
-
- SIM_PAIRWISE_DAG_EDGE_LI_2003 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Pekar_Staab_2002 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Pekar V, Staab S: Taxonomy learning: factoring the structure of a taxonomy
into a semantic classification decision.
- Sim_pairwise_DAG_edge_Pekar_Staab_2002() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Pekar_Staab_2002
-
- SIM_PAIRWISE_DAG_EDGE_PEKAR_STAAB_2002 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Rada_1989 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Rada R, Mili H, Bicknell E, Blettner M: Development and application of a
metric on semantic nets.
- Sim_pairwise_DAG_edge_Rada_1989() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_1989
-
- SIM_PAIRWISE_DAG_EDGE_RADA_1989 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Rada_LCA_1989 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Rada R, Mili H, Bicknell E, Blettner M: Development and application of a
metric on semantic nets.
- Sim_pairwise_DAG_edge_Rada_LCA_1989() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Rada_LCA_1989
-
- SIM_PAIRWISE_DAG_EDGE_RADA_LCA_1989 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Resnik_1995 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental
-
Faites au feeling par seb, verifier quelle est proche de celle de resnik
- Sim_pairwise_DAG_edge_Resnik_1995() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_Resnik_1995
-
- SIM_PAIRWISE_DAG_EDGE_RESNIK_1995 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Slimani_2006 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental
-
Slimani T, Boutheina BY, Mellouli K: A New Similarity Measure based on
Edge Counting.
- Sim_pairwise_DAG_edge_Slimani_2006() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental.Sim_pairwise_DAG_edge_Slimani_2006
-
- SIM_PAIRWISE_DAG_EDGE_SLIMANI_2006 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Stojanovic_2001 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Stojanovic N, Alexander M, Staab S, Rudi S, York S: SEAL - A Framework for
Developing SEmantic PortALs.
- Sim_pairwise_DAG_edge_Stojanovic_2001() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Stojanovic_2001
-
- SIM_PAIRWISE_DAG_EDGE_STOJANOVIC_2001 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_edge_Wu_Palmer_1994 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
Wu Z, Palmer M: Verb semantics and lexical selection.
- Sim_pairwise_DAG_edge_Wu_Palmer_1994() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.Sim_pairwise_DAG_edge_Wu_Palmer_1994
-
- SIM_PAIRWISE_DAG_EDGE_WU_PALMER_1994 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_HYBRID_BASED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_hybrid_Ranwez_2006 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental
-
Ranwez S, Ranwez V, Villerd J, Crampes M: Ontological Distance Measures
for Information Visualisation on Conceptual Maps.
- Sim_pairwise_DAG_hybrid_Ranwez_2006() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental.Sim_pairwise_DAG_hybrid_Ranwez_2006
-
- SIM_PAIRWISE_DAG_HYBRID_RANWEZ_2006 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_hybrid_Wang_2007 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental
-
Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F: A new method to measure the semantic similarity of GO terms.
- Sim_pairwise_DAG_hybrid_Wang_2007() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental.Sim_pairwise_DAG_hybrid_Wang_2007
-
- SIM_PAIRWISE_DAG_NODE_BASED - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Constants - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
- Sim_pairwise_DAG_node_Constants() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Constants
-
- Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Feature-based formulation of the Tversky Ratio Model.
- Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model
-
- Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model(double, double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model
-
Create a Tversky measure specifying gamma, alpha and beta parameters
- SIM_PAIRWISE_DAG_NODE_FEATURE_TVERSKY_CONTRAST_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Feature-based formulation of the Tversky Ratio Model.
- Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model
-
- Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model(double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model
-
Create a Tversky measure specifying alpha and beta parameters
- SIM_PAIRWISE_DAG_NODE_FEATURE_TVERSKY_RATIO_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_GL - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Gower and Legendre IC-based abstract expression.
- Sim_pairwise_DAG_node_GL() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_GL
-
- SIM_PAIRWISE_DAG_NODE_GL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_GL_GraSM - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_GL_GraSM() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_GL_GraSM
-
- SIM_PAIRWISE_DAG_NODE_GL_GRASM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Harispe_2013 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_Harispe_2013() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Harispe_2013
-
- SIM_PAIRWISE_DAG_NODE_HARISPE_2013 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_IC_ANNOT - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_IC_INTRINSIC - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of Tversky Ratio Model
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model(double, double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model
-
Create a Tversky measure specifying gamma, alpha and beta parameters
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of Tversky Ratio Model
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model
-
- Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model(double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model
-
Create a Tversky measure specifying alpha and beta parameters
- Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of Tversky Ratio Model
- Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
- Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model(double, double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model
-
Create a Tversky measure specifying gamma, alpha and beta parameters
- Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of Tversky Ratio Model
- Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model
-
- Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model(double, double) - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model
-
Create a Tversky measure specifying alpha and beta parameters
- Sim_pairwise_DAG_node_Jaccard_3W_IC - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of the Jaccard measure.
- Sim_pairwise_DAG_node_Jaccard_3W_IC() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_3W_IC
-
- SIM_PAIRWISE_DAG_NODE_JACCARD_3W_IC - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Jaccard_IC - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
IC formulation of the Jaccard measure.
- Sim_pairwise_DAG_node_Jaccard_IC() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jaccard_IC
-
- SIM_PAIRWISE_DAG_NODE_JACCARD_IC - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Jiang_Conrath_1997 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Jiang J, Conrath D: Semantic Similarity Based on Corpus Statistics and
Lexical Taxonomy.
- Sim_pairwise_DAG_node_Jiang_Conrath_1997() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997
-
- SIM_PAIRWISE_DAG_NODE_JIANG_CONRATH_1997 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Jiang J, Conrath D: Semantic Similarity Based on Corpus Statistics and
Lexical Taxonomy.
- Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm
-
- SIM_PAIRWISE_DAG_NODE_JIANG_CONRATH_1997_NORM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Lin_1998 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Implementation of the measure proposed by Lin for comparing two concepts
defined in a taxonomy.
- Sim_pairwise_DAG_node_Lin_1998() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Lin_1998
-
- SIM_PAIRWISE_DAG_NODE_LIN_1998 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Lin_1998_GraSM - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
Lin D: An Information-Theoretic Definition of Similarity.
- Sim_pairwise_DAG_node_Lin_1998_GraSM() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Lin_1998_GraSM
-
- SIM_PAIRWISE_DAG_NODE_LIN_1998_GraSM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Mazandu_2012 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
Implementation of the Universal similarity measure i.e.
- Sim_pairwise_DAG_node_Mazandu_2012() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Mazandu_2012
-
- SIM_PAIRWISE_DAG_NODE_MAZANDU_2012 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Resnik_1995 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Resnik P: Using Information Content to Evaluate Semantic Similarity in a
Taxonomy.
- Sim_pairwise_DAG_node_Resnik_1995() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Resnik_1995
-
- SIM_PAIRWISE_DAG_NODE_RESNIK_1995 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Resnik_1995_Ancestors - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
Resnik P: Using Information Content to Evaluate Semantic Similarity in a
Taxonomy.
- Sim_pairwise_DAG_node_Resnik_1995_Ancestors() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Resnik_1995_Ancestors
-
- SIM_PAIRWISE_DAG_NODE_RESNIK_1995_ANCESTORS - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Resnik_1995_Descendants - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
Resnik P: Using Information Content to Evaluate Semantic Similarity in a
Taxonomy.
- Sim_pairwise_DAG_node_Resnik_1995_Descendants() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Resnik_1995_Descendants
-
- SIM_PAIRWISE_DAG_NODE_RESNIK_1995_DESCENDANTS - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Resnik_1995_GraSM - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
Resnik P: Using Information Content to Evaluate Semantic Similarity in a
Taxonomy.
- Sim_pairwise_DAG_node_Resnik_1995_GraSM() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Resnik_1995_GraSM
-
- SIM_PAIRWISE_DAG_NODE_RESNIK_1995_GraSM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_SCHLICKER_2006 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Schlicker_2006_SimRel - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Schlicker, Andreas, et al.
- Sim_pairwise_DAG_node_Schlicker_2006_SimRel() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Schlicker_2006_SimRel
-
- SIM_PAIRWISE_DAG_NODE_SCHLICKER_3WJACCARD - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel
-
- SIM_PAIRWISE_DAG_NODE_SCHLICKER_GL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Schlicker_GL_SimRel - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_Schlicker_GL_SimRel() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_GL_SimRel
-
- SIM_PAIRWISE_DAG_NODE_SCHLICKER_JACCARD - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel
-
- SIM_PAIRWISE_DAG_NODE_SCHLICKER_TVERSKY - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental.Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel
-
- Sim_pairwise_DAG_node_Sim_IC_2010 - Class in slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
Effectively integrating information content and structural relationship to
improve the GO-based similarity measure between proteins.
- Sim_pairwise_DAG_node_Sim_IC_2010() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.node_based.Sim_pairwise_DAG_node_Sim_IC_2010
-
- SIM_PAIRWISE_DAG_NODE_SIM_IC_2010 - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_TVERSKY_IC_CONTRAST_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_TVERSKY_IC_PROP_CONTRAST_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_TVERSKY_IC_PROP_RATIO_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_DAG_NODE_TVERSKY_IC_RATIO_MODEL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_GENERAL - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- Sim_pairwise_Random - Class in slib.sml.sm.core.measures.others.pairwise
-
Random measure for tests
- Sim_pairwise_Random() - Constructor for class slib.sml.sm.core.measures.others.pairwise.Sim_pairwise_Random
-
- SIM_PAIRWISE_RANDOM - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SIM_PAIRWISE_SHORT_FLAG - Static variable in class slib.sml.sm.core.utils.SMConstants
-
- SimDagEdgeUtils - Class in slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils
-
Utility class for edge-based measures.
- SimDagEdgeUtils() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils.SimDagEdgeUtils
-
- SimDagHybridUtils - Class in slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.utils
-
- SimDagHybridUtils() - Constructor for class slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.utils.SimDagHybridUtils
-
- simManager - Variable in class slib.tools.smltoolkit.sm.cli.core.SmCli
-
- slib.examples.graph.traversal - package slib.examples.graph.traversal
-
- slib.examples.sml.general - package slib.examples.sml.general
-
- slib.examples.sml.go - package slib.examples.sml.go
-
- slib.examples.sml.mesh - package slib.examples.sml.mesh
-
- slib.examples.sml.owl - package slib.examples.sml.owl
-
- slib.examples.sml.snomedct - package slib.examples.sml.snomedct
-
- slib.examples.sml.wordnet - package slib.examples.sml.wordnet
-
- slib.examples.sml.yago - package slib.examples.sml.yago
-
- slib.graph.algo - package slib.graph.algo
-
- slib.graph.algo.accessor - package slib.graph.algo.accessor
-
- slib.graph.algo.extraction - package slib.graph.algo.extraction
-
- slib.graph.algo.extraction.metric - package slib.graph.algo.extraction.metric
-
- slib.graph.algo.extraction.reduction.dag - package slib.graph.algo.extraction.reduction.dag
-
- slib.graph.algo.extraction.rvf - package slib.graph.algo.extraction.rvf
-
- slib.graph.algo.extraction.rvf.instances - package slib.graph.algo.extraction.rvf.instances
-
- slib.graph.algo.extraction.rvf.instances.impl - package slib.graph.algo.extraction.rvf.instances.impl
-
- slib.graph.algo.extraction.shortest_path - package slib.graph.algo.extraction.shortest_path
-
- slib.graph.algo.extraction.traversal - package slib.graph.algo.extraction.traversal
-
- slib.graph.algo.extraction.traversal.classical - package slib.graph.algo.extraction.traversal.classical
-
- slib.graph.algo.extraction.utils - package slib.graph.algo.extraction.utils
-
- slib.graph.algo.extraction.validator.dag - package slib.graph.algo.extraction.validator.dag
-
- slib.graph.algo.metric - package slib.graph.algo.metric
-
- slib.graph.algo.reduction.dag - package slib.graph.algo.reduction.dag
-
- slib.graph.algo.shortest_path - package slib.graph.algo.shortest_path
-
- slib.graph.algo.traversal - package slib.graph.algo.traversal
-
- slib.graph.algo.traversal.classical - package slib.graph.algo.traversal.classical
-
- slib.graph.algo.utils - package slib.graph.algo.utils
-
- slib.graph.algo.validator.dag - package slib.graph.algo.validator.dag
-
- slib.graph.io.conf - package slib.graph.io.conf
-
- slib.graph.io.loader - package slib.graph.io.loader
-
- slib.graph.io.loader.annot - package slib.graph.io.loader.annot
-
- slib.graph.io.loader.bio.gaf2 - package slib.graph.io.loader.bio.gaf2
-
- slib.graph.io.loader.bio.mesh - package slib.graph.io.loader.bio.mesh
-
- slib.graph.io.loader.bio.obo - package slib.graph.io.loader.bio.obo
-
- slib.graph.io.loader.bio.obo.utils - package slib.graph.io.loader.bio.obo.utils
-
- slib.graph.io.loader.bio.snomedct - package slib.graph.io.loader.bio.snomedct
-
- slib.graph.io.loader.csv - package slib.graph.io.loader.csv
-
- slib.graph.io.loader.rdf - package slib.graph.io.loader.rdf
-
- slib.graph.io.loader.slibformat - package slib.graph.io.loader.slibformat
-
- slib.graph.io.loader.utils.filter.graph - package slib.graph.io.loader.utils.filter.graph
-
- slib.graph.io.loader.utils.filter.graph.gaf2 - package slib.graph.io.loader.utils.filter.graph.gaf2
-
- slib.graph.io.loader.utils.filter.graph.metrics - package slib.graph.io.loader.utils.filter.graph.metrics
-
- slib.graph.io.loader.utils.filter.graph.repo - package slib.graph.io.loader.utils.filter.graph.repo
-
- slib.graph.io.loader.wordnet - package slib.graph.io.loader.wordnet
-
- slib.graph.io.plotter - package slib.graph.io.plotter
-
- slib.graph.io.util - package slib.graph.io.util
-
- slib.graph.model.graph - package slib.graph.model.graph
-
- slib.graph.model.graph.elements - package slib.graph.model.graph.elements
-
- slib.graph.model.graph.utils - package slib.graph.model.graph.utils
-
- slib.graph.model.graph.weight - package slib.graph.model.graph.weight
-
- slib.graph.model.impl.graph.elements - package slib.graph.model.impl.graph.elements
-
- slib.graph.model.impl.graph.memory - package slib.graph.model.impl.graph.memory
-
- slib.graph.model.impl.graph.weight - package slib.graph.model.impl.graph.weight
-
- slib.graph.model.impl.repo - package slib.graph.model.impl.repo
-
- slib.graph.model.impl.utils - package slib.graph.model.impl.utils
-
- slib.graph.model.repo - package slib.graph.model.repo
-
- slib.graph.utils - package slib.graph.utils
-
- slib.indexer - package slib.indexer
-
- slib.indexer.mesh - package slib.indexer.mesh
-
- slib.indexer.obo - package slib.indexer.obo
-
- slib.indexer.snomed_ct - package slib.indexer.snomed_ct
-
- slib.indexer.wordnet - package slib.indexer.wordnet
-
- slib.sml - package slib.sml
-
- slib.sml.sm - package slib.sml.sm
-
- slib.sml.sm.core.engine - package slib.sml.sm.core.engine
-
- slib.sml.sm.core.measures - package slib.sml.sm.core.measures
-
- slib.sml.sm.core.measures.corpus - package slib.sml.sm.core.measures.corpus
-
- slib.sml.sm.core.measures.graph.framework.dag - package slib.sml.sm.core.measures.graph.framework.dag
-
- slib.sml.sm.core.measures.graph.groupwise.dag - package slib.sml.sm.core.measures.graph.groupwise.dag
-
- slib.sml.sm.core.measures.graph.pairwise.dag - package slib.sml.sm.core.measures.graph.pairwise.dag
-
- slib.sml.sm.core.measures.graph.pairwise.dag.edge_based - package slib.sml.sm.core.measures.graph.pairwise.dag.edge_based
-
- slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental - package slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.experimental
-
- slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils - package slib.sml.sm.core.measures.graph.pairwise.dag.edge_based.utils
-
- slib.sml.sm.core.measures.graph.pairwise.dag.hybrid - package slib.sml.sm.core.measures.graph.pairwise.dag.hybrid
-
- slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental - package slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.experimental
-
- slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.utils - package slib.sml.sm.core.measures.graph.pairwise.dag.hybrid.utils
-
- slib.sml.sm.core.measures.graph.pairwise.dag.node_based - package slib.sml.sm.core.measures.graph.pairwise.dag.node_based
-
- slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental - package slib.sml.sm.core.measures.graph.pairwise.dag.node_based.experimental
-
- slib.sml.sm.core.measures.others.groupwise.direct - package slib.sml.sm.core.measures.others.groupwise.direct
-
- slib.sml.sm.core.measures.others.groupwise.direct.vector - package slib.sml.sm.core.measures.others.groupwise.direct.vector
-
- slib.sml.sm.core.measures.others.groupwise.indirect - package slib.sml.sm.core.measures.others.groupwise.indirect
-
- slib.sml.sm.core.measures.others.groupwise.indirect.experimental - package slib.sml.sm.core.measures.others.groupwise.indirect.experimental
-
- slib.sml.sm.core.measures.others.pairwise - package slib.sml.sm.core.measures.others.pairwise
-
- slib.sml.sm.core.measures.string - package slib.sml.sm.core.measures.string
-
- slib.sml.sm.core.measures.vector - package slib.sml.sm.core.measures.vector
-
- slib.sml.sm.core.metrics.ic - package slib.sml.sm.core.metrics.ic
-
- slib.sml.sm.core.metrics.ic.annot - package slib.sml.sm.core.metrics.ic.annot
-
- slib.sml.sm.core.metrics.ic.topo - package slib.sml.sm.core.metrics.ic.topo
-
- slib.sml.sm.core.metrics.ic.utils - package slib.sml.sm.core.metrics.ic.utils
-
- slib.sml.sm.core.metrics.utils - package slib.sml.sm.core.metrics.utils
-
- slib.sml.sm.core.metrics.vector - package slib.sml.sm.core.metrics.vector
-
- slib.sml.sm.core.utils - package slib.sml.sm.core.utils
-
- slib.sml.smutils - package slib.sml.smutils
-
- slib.tools.module - package slib.tools.module
-
- slib.tools.ontofocus.cli - package slib.tools.ontofocus.cli
-
- slib.tools.ontofocus.cli.debug - package slib.tools.ontofocus.cli.debug
-
- slib.tools.ontofocus.cli.utils - package slib.tools.ontofocus.cli.utils
-
- slib.tools.ontofocus.core - package slib.tools.ontofocus.core
-
- slib.tools.ontofocus.core.utils - package slib.tools.ontofocus.core.utils
-
- slib.tools.smltoolkit - package slib.tools.smltoolkit
-
- slib.tools.smltoolkit.sm.cli.conf.xml.loader - package slib.tools.smltoolkit.sm.cli.conf.xml.loader
-
- slib.tools.smltoolkit.sm.cli.conf.xml.utils - package slib.tools.smltoolkit.sm.cli.conf.xml.utils
-
- slib.tools.smltoolkit.sm.cli.core - package slib.tools.smltoolkit.sm.cli.core
-
- slib.tools.smltoolkit.sm.cli.core.cmd - package slib.tools.smltoolkit.sm.cli.core.cmd
-
- slib.tools.smltoolkit.sm.cli.core.utils - package slib.tools.smltoolkit.sm.cli.core.utils
-
- slib.tools.smltoolkit.sm.cli.core.utils.calc - package slib.tools.smltoolkit.sm.cli.core.utils.calc
-
- slib.tools.smltoolkit.sm.cli.profile.go - package slib.tools.smltoolkit.sm.cli.profile.go
-
- slib.tools.smltoolkit.sm.cli.profile.mesh - package slib.tools.smltoolkit.sm.cli.profile.mesh
-
- slib.utils - package slib.utils
-
- slib.utils.ex - package slib.utils.ex
-
- slib.utils.i - package slib.utils.i
-
- slib.utils.impl - package slib.utils.impl
-
- slib.utils.threads - package slib.utils.threads
-
- SLIB_Ex_Critic - Exception in slib.utils.ex
-
- SLIB_Ex_Critic(String) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
-
- SLIB_Ex_Critic(Throwable) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
-
- SLIB_Ex_Critic(String, Throwable) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
-
- SLIB_Ex_Warning - Exception in slib.utils.ex
-
- SLIB_Ex_Warning(String) - Constructor for exception slib.utils.ex.SLIB_Ex_Warning
-
- SLIB_Exception - Exception in slib.utils.ex
-
- SLIB_Exception(String) - Constructor for exception slib.utils.ex.SLIB_Exception
-
- SLIB_Exception(Throwable) - Constructor for exception slib.utils.ex.SLIB_Exception
-
- SLIB_Exception(String, Throwable) - Constructor for exception slib.utils.ex.SLIB_Exception
-
- SlibRdfHandler - Class in slib.graph.io.loader.rdf
-
- SlibRdfHandler(G) - Constructor for class slib.graph.io.loader.rdf.SlibRdfHandler
-
- SM_Engine - Class in slib.sml.sm.core.engine
-
This class defines a Semantic Measures Engine which gives access to several
methods commonly used to define ontology-based semantic measures.
- SM_Engine(G) - Constructor for class slib.sml.sm.core.engine.SM_Engine
-
Constructor of an engine associated to the given graph.
- Sm_XML_Cst - Class in slib.tools.smltoolkit.sm.cli.conf.xml.utils
-
- Sm_XML_Cst() - Constructor for class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
-
- Sm_XMLConfLoader - Class in slib.tools.smltoolkit.sm.cli.conf.xml.loader
-
- Sm_XMLConfLoader(String) - Constructor for class slib.tools.smltoolkit.sm.cli.conf.xml.loader.Sm_XMLConfLoader
-
- SmCli - Class in slib.tools.smltoolkit.sm.cli.core
-
- SmCli() - Constructor for class slib.tools.smltoolkit.sm.cli.core.SmCli
-
- SmCmdHandler - Class in slib.tools.smltoolkit.sm.cli.core.cmd
-
- SmCmdHandler() - Constructor for class slib.tools.smltoolkit.sm.cli.core.cmd.SmCmdHandler
-
- SmCmdHandlerCst - Class in slib.tools.smltoolkit.sm.cli.core.cmd
-
- SmCmdHandlerCst() - Constructor for class slib.tools.smltoolkit.sm.cli.core.cmd.SmCmdHandlerCst
-
- SMComputation - Class in slib.examples.sml.general
-
Example of a Semantic measure computation using the Semantic Measures Library.
- SMComputation() - Constructor for class slib.examples.sml.general.SMComputation
-
- SMComputationGO_extrinsic_IC - Class in slib.examples.sml.go
-
Example which shows how to use the Semantic Measures Library to compute
the Information Content (IC) of Gene Ontology terms using an Extrinsic IC
(e.g.
- SMComputationGO_extrinsic_IC() - Constructor for class slib.examples.sml.go.SMComputationGO_extrinsic_IC
-
- SMComputationGO_groupwise - Class in slib.examples.sml.go
-
Example of a Semantic measure computation using the Semantic Measures
Library.
- SMComputationGO_groupwise() - Constructor for class slib.examples.sml.go.SMComputationGO_groupwise
-
- SMComputationGO_groupwise_million - Class in slib.examples.sml.go
-
Example of a Semantic measure computation using the Semantic Measures
Library.
- SMComputationGO_groupwise_million() - Constructor for class slib.examples.sml.go.SMComputationGO_groupwise_million
-
- SMComputationGO_pairwise - Class in slib.examples.sml.go
-
Example of a Semantic measure computation using the Semantic Measures
Library.
- SMComputationGO_pairwise() - Constructor for class slib.examples.sml.go.SMComputationGO_pairwise
-
- SMComputationGO_pairwise_edge_based - Class in slib.examples.sml.go
-
Example of a Semantic measure computation using the Semantic Measures
Library.
- SMComputationGO_pairwise_edge_based() - Constructor for class slib.examples.sml.go.SMComputationGO_pairwise_edge_based
-
- SMComputationOWL - Class in slib.examples.sml.owl
-
- SMComputationOWL() - Constructor for class slib.examples.sml.owl.SMComputationOWL
-
- SMComputationSnomedCT - Class in slib.examples.sml.snomedct
-
Example of a Semantic measure computation using the Semantic Measures
Library.
- SMComputationSnomedCT() - Constructor for class slib.examples.sml.snomedct.SMComputationSnomedCT
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- SMComputationYago - Class in slib.examples.sml.yago
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- SMComputationYago() - Constructor for class slib.examples.sml.yago.SMComputationYago
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- SMconf - Class in slib.sml.sm.core.utils
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Representation of the configuration of a semantic measure.
- SMconf(String) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given flag.
- SMconf(String, String) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given id and flag.
- SMconf(String, String, String) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given id, flag and
label.
- SMconf(String, ICconf) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given flag and
Information Content configuration.
- SMconf(String, String, ICconf) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given flag and
Information Content configuration.
- SMconf(String, String, String, ICconf) - Constructor for class slib.sml.sm.core.utils.SMconf
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Build an instance of configuration considering the given id, flag and
Information Content configuration.
- SMConstants - Class in slib.sml.sm.core.utils
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Class used to defined Semantic Measures constants such as measures flags.
- SMConstants() - Constructor for class slib.sml.sm.core.utils.SMConstants
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- SML_MODULE - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
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- SML_SM - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
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- SML_SM_include - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
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- SML_SM_module_XML_block_conf - Class in slib.tools.smltoolkit.sm.cli.core.utils
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- SML_SM_module_XML_block_conf() - Constructor for class slib.tools.smltoolkit.sm.cli.core.utils.SML_SM_module_XML_block_conf
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- SML_TAG - Static variable in class slib.tools.smltoolkit.sm.cli.conf.xml.utils.Sm_XML_Cst
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- SmlModuleCLI - Interface in slib.tools.smltoolkit
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- SmlToolKitCli - Class in slib.tools.smltoolkit
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Semantic Measures Library Toolkit Command Line Interface
- SmlToolKitCli() - Constructor for class slib.tools.smltoolkit.SmlToolKitCli
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- SmlToolKitCliCst - Class in slib.tools.smltoolkit
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- SmlToolKitCliCst() - Constructor for class slib.tools.smltoolkit.SmlToolKitCliCst
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- SmlToolKitCst - Class in slib.tools.smltoolkit
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Constant of the Semantic Framework Module
- SmlToolKitCst() - Constructor for class slib.tools.smltoolkit.SmlToolKitCst
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- SMParams - Enum in slib.sml.sm.core.utils
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- SmProfile_GO - Class in slib.tools.smltoolkit.sm.cli.profile.go
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- SmProfile_GO() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.go.SmProfile_GO
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- SmProfile_MeSH - Class in slib.tools.smltoolkit.sm.cli.profile.mesh
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- SmProfile_MeSH() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.mesh.SmProfile_MeSH
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- SmProfileGOCst - Class in slib.tools.smltoolkit.sm.cli.profile.go
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- SmProfileGOCst() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.go.SmProfileGOCst
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- SmProfileGOHandler - Class in slib.tools.smltoolkit.sm.cli.profile.go
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- SmProfileGOHandler() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.go.SmProfileGOHandler
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- SmProfileMeSHCst - Class in slib.tools.smltoolkit.sm.cli.profile.mesh
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- SmProfileMeSHCst() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.mesh.SmProfileMeSHCst
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- SmProfileMeSHHandler - Class in slib.tools.smltoolkit.sm.cli.profile.mesh
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- SmProfileMeSHHandler(String[]) - Constructor for class slib.tools.smltoolkit.sm.cli.profile.mesh.SmProfileMeSHHandler
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- SMProxResultStorage - Class in slib.sml.sm.core.engine
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- SMProxResultStorage() - Constructor for class slib.sml.sm.core.engine.SMProxResultStorage
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- SMQueryParam - Class in slib.tools.smltoolkit.sm.cli.core.utils
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- SMQueryParam(String) - Constructor for class slib.tools.smltoolkit.sm.cli.core.utils.SMQueryParam
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- SmToolkitCst - Class in slib.tools.smltoolkit.sm.cli.core.utils
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- SmToolkitCst() - Constructor for class slib.tools.smltoolkit.sm.cli.core.utils.SmToolkitCst
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- SmToolkitGOCst - Class in slib.tools.smltoolkit.sm.cli.profile.go
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- SmToolkitGOCst() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.go.SmToolkitGOCst
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- SmToolkitMeSHCst - Class in slib.tools.smltoolkit.sm.cli.profile.mesh
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- SmToolkitMeSHCst() - Constructor for class slib.tools.smltoolkit.sm.cli.profile.mesh.SmToolkitMeSHCst
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- SMutils - Class in slib.sml.sm.core.utils
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Class used to define utility methods.
- SMutils() - Constructor for class slib.sml.sm.core.utils.SMutils
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- SMutils - Class in slib.tools.smltoolkit.sm.cli.core.utils
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- SMutils() - Constructor for class slib.tools.smltoolkit.sm.cli.core.utils.SMutils
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- splitSize_default - Static variable in class slib.sml.smutils.ResultsMerger
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- splitString(String, int) - Static method in class slib.graph.io.plotter.GraphPlotter_Graphviz
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- SQLiteUtils - Class in slib.sml.smutils
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Class used to process large SME results files through SQLlite databases
Processed file must respect the following restrictions: - tab separated
format - containing a header (first non-empty line which do not start with !
).
- SQLiteUtils() - Constructor for class slib.sml.smutils.SQLiteUtils
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- start() - Method in class slib.utils.impl.Timer
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- startElement(String, String, String, Attributes) - Method in class slib.graph.io.loader.bio.mesh.MeshXMLHandler
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- startElement(String, String, String, Attributes) - Method in class slib.indexer.mesh.MeshXMLHandler
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- startRDF() - Method in class slib.graph.io.loader.rdf.SlibRdfHandler
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- StatementTemplate_Constraint_Type - Enum in slib.graph.io.loader.csv
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- StatementTemplateElement - Enum in slib.graph.io.loader.csv
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- STM_ATT_OBJECT - Static variable in class slib.tools.module.XmlTags
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- STM_ATT_PREDICATE - Static variable in class slib.tools.module.XmlTags
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- STM_ATT_SUBJECT - Static variable in class slib.tools.module.XmlTags
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- STM_CONSTRAINT_ATT_ELEMENT - Static variable in class slib.tools.module.XmlTags
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- STM_CONSTRAINT_ATT_TYPE - Static variable in class slib.tools.module.XmlTags
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- STM_CONSTRAINT_TAG - Static variable in class slib.tools.module.XmlTags
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- STM_TAG - Static variable in class slib.tools.module.XmlTags
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- stop() - Method in class slib.utils.impl.Timer
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- stringToBoolean(String) - Static method in class slib.utils.impl.Util
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Convert the given
String to a boolean value.
- stringToDouble(String) - Static method in class slib.utils.impl.Util
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- stringToInteger(String) - Static method in class slib.utils.impl.Util
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- stringToLong(String) - Static method in class slib.utils.impl.Util
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- supportedFormat - Static variable in class slib.graph.io.loader.GraphLoaderGeneric
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The formats currently supported by the generic loader.
- supportedTypes - Static variable in class slib.graph.io.loader.utils.filter.graph.FilterCst
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- supportFormat(String) - Static method in class slib.graph.io.loader.GraphLoaderGeneric
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Check if the generic loader support the given format.
- supportType(String) - Static method in class slib.tools.module.FilterBuilderGeneric
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- valid(GAction) - Static method in class slib.graph.algo.extraction.utils.GActionValidator
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Test if the given
GAction is valid.
- valid(GAction) - Static method in class slib.graph.algo.utils.GActionValidator
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Test if the given
GAction is valid.
- valid(GAction) - Static method in class slib.graph.io.util.GActionValidator
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- valid(GDataConf) - Static method in class slib.graph.io.util.GDataValidator
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- ValidatorDAG - Class in slib.graph.algo.extraction.validator.dag
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Used to validate if a graph is directed and acyclic (DAG)
- ValidatorDAG() - Constructor for class slib.graph.algo.extraction.validator.dag.ValidatorDAG
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- ValidatorDAG - Class in slib.graph.algo.validator.dag
-
Used to validate if a graph is directed and acyclic (DAG)
- ValidatorDAG() - Constructor for class slib.graph.algo.validator.dag.ValidatorDAG
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- VALUE - Static variable in class slib.graph.io.loader.utils.filter.graph.metrics.FilterGraph_Metrics_cst
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- Value_ - Variable in class slib.utils.Pair
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- VALUE_ATTR - Static variable in class slib.tools.module.XmlTags
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- valueOf(String) - Static method in enum slib.graph.algo.extraction.utils.Color
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.algo.extraction.utils.GActionType
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.algo.utils.Color
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.algo.utils.GActionType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.io.loader.csv.StatementTemplate_Constraint_Type
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.io.loader.csv.StatementTemplateElement
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.io.util.GFormat
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.graph.model.graph.utils.Direction
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.sml.sm.core.measures.corpus.MatrixType
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.sml.sm.core.measures.MType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.sml.sm.core.utils.SMParams
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum slib.tools.smltoolkit.sm.cli.core.utils.ActionsParams
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum slib.graph.algo.extraction.utils.Color
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.algo.extraction.utils.GActionType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.algo.utils.Color
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.algo.utils.GActionType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.io.loader.csv.StatementTemplate_Constraint_Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.io.loader.csv.StatementTemplateElement
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.io.util.GFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.graph.model.graph.utils.Direction
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.sml.sm.core.measures.corpus.MatrixType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.sml.sm.core.measures.MType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.sml.sm.core.utils.SMParams
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum slib.tools.smltoolkit.sm.cli.core.utils.ActionsParams
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- VARIABLE_TAG - Static variable in class slib.tools.module.XmlTags
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- VARIABLES_TAG - Static variable in class slib.tools.module.XmlTags
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- VectorSpaceModel - Class in slib.sml.sm.core.measures.others.groupwise.direct.vector
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- VectorSpaceModel() - Constructor for class slib.sml.sm.core.measures.others.groupwise.direct.vector.VectorSpaceModel
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- VectorWeight_Chabalier_2007 - Class in slib.sml.sm.core.metrics.vector
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- VectorWeight_Chabalier_2007() - Constructor for class slib.sml.sm.core.metrics.vector.VectorWeight_Chabalier_2007
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- VectorWeight_Chabalier_Propaggated - Class in slib.sml.sm.core.metrics.vector
-
- VectorWeight_Chabalier_Propaggated() - Constructor for class slib.sml.sm.core.metrics.vector.VectorWeight_Chabalier_Propaggated
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- version - Variable in class slib.tools.module.ModuleCst
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- version - Static variable in class slib.tools.smltoolkit.SmlToolKitCliCst
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- versionSnapshot - Variable in class slib.tools.module.ModuleCst
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- VocContextMatrixBuilder - Class in slib.sml.sm.core.measures.corpus
-
- VocContextMatrixBuilder(MatrixType, Set<String>) - Constructor for class slib.sml.sm.core.measures.corpus.VocContextMatrixBuilder
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- VocContextMatrixBuilder(MatrixType, Set<String>, List<String>) - Constructor for class slib.sml.sm.core.measures.corpus.VocContextMatrixBuilder
-