public abstract class AbstractOwlSim extends Object implements OwlSim
OwlSim.ScoreAttributeSetPair, OwlSim.Stat, OwlSim.StatsPerIndividual
Modifier and Type | Field and Description |
---|---|
protected Integer |
corpusSize |
EnrichmentConfig |
enrichmentConfig |
String |
icIRIString |
protected boolean |
isDisableLCSCache |
protected boolean |
isLCSCacheFullyPopulated |
protected boolean |
isNoLookupForLCSCache |
HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> |
metricStatMaxes |
HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> |
metricStatMeans |
HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> |
metricStatMins |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
overallStats |
OwlSim.StatsPerIndividual |
overallSummaryStatsPerIndividual |
protected org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
SimStats |
simStats |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
simStatsPerIndividual |
HashMap<org.semanticweb.owlapi.model.OWLClass,OwlSim.StatsPerIndividual> |
subgraphSummaryStatsPerIndividual |
Constructor and Description |
---|
AbstractOwlSim() |
Modifier and Type | Method and Description |
---|---|
void |
assignDefaultInformationContentForAllClasses() |
org.semanticweb.owlapi.model.OWLOntology |
cacheInformationContentInOntology()
Generates an ontology containing annotation assertion axioms connecting
a class to an IC value.
|
List<EnrichmentResult> |
calculateAllByAllEnrichment() |
List<EnrichmentResult> |
calculateAllByAllEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass pc1,
org.semanticweb.owlapi.model.OWLClass pc2)
For every c ∈ sample set, test c against all classes ∈ enriched class set.
|
void |
calculateCombinedScore(ElementPairScores s,
double maxMaxIC,
double maxBMA) |
List<EnrichmentResult> |
calculateEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass sampleSetClass)
|
double |
calculateOverallAnnotationSufficiencyForAttributeSet(Set<org.semanticweb.owlapi.model.OWLClass> atts) |
double |
calculateOverallAnnotationSufficiencyForIndividual(org.semanticweb.owlapi.model.OWLNamedIndividual i) |
EnrichmentResult |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass)
Pairwise enrichment test
|
double |
calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<org.semanticweb.owlapi.model.OWLClass> atts,
org.semanticweb.owlapi.model.OWLClass c) |
double |
calculateSubgraphAnnotationSufficiencyForIndividual(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c) |
protected abstract void |
clearInformationContentCache() |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
computeAttributeSetSimilarityStats(Set<org.semanticweb.owlapi.model.OWLClass> atts) |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
computeAttributeSetSimilarityStatsForSubgraph(Set<org.semanticweb.owlapi.model.OWLClass> atts,
org.semanticweb.owlapi.model.OWLClass sub) |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
computeIndividualSimilarityStats(org.semanticweb.owlapi.model.OWLNamedIndividual i) |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
computeIndividualStats(org.semanticweb.owlapi.model.OWLNamedIndividual i)
This will compute the individual summary statistics over the
set of anntoated classes to an individual i.
|
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
computeIndividualStatsForSubgraph(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c) |
void |
computeSystemStats()
This function will compute the IC-based summary statistics over the set of
individuals for direct annotations.
|
void |
computeSystemStatsForSubgraph(org.semanticweb.owlapi.model.OWLClass c) |
void |
dispose()
call when owlsim object is no longer required
|
List<EnrichmentResult> |
filterEnrichmentResults(List<EnrichmentResult> resultsIn) |
List<ElementPairScores> |
findMatches(org.semanticweb.owlapi.model.OWLNamedIndividual i,
String targetIdSpace) |
List<ElementPairScores> |
findMatches(org.semanticweb.owlapi.model.OWLNamedIndividual i,
String targetIdSpace,
double minSimJPct,
double minMaxIC) |
List<ElementPairScores> |
findMatches(Set<org.semanticweb.owlapi.model.OWLClass> atts,
String targetIdSpace)
Find all similar matches to a pseudo-individual with a set of attributes
when compared to loaded individuals using
getGroupwiseSimilarity
with default cutoffs. |
int |
getAsymmetricAttributeJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLClass a,
org.semanticweb.owlapi.model.OWLClass b)
Equivalent to
OwlSim.getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) * 100 |
int |
getAsymmetricElementJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
|
int |
getAttributeJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLClass a,
org.semanticweb.owlapi.model.OWLClass b)
Equivalent to
OwlSim.getAttributeJaccardSimilarity(OWLClass, OWLClass) * 100 |
double |
getConditionalProbability(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
int |
getCorpusSize()
The number of entities in the entire set being analyzed.
|
int |
getElementJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
Equivalent to
OwlSim.getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) * 100 |
EnrichmentConfig |
getEnrichmentConfig() |
Double |
getEntropy() |
Double |
getEntropy(Set<org.semanticweb.owlapi.model.OWLClass> cset) |
ElementPairScores |
getGroupwiseSimilarity(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
Compare two named individuals
(i,j) . |
void |
getICSimDisj(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
OwlSim.ScoreAttributeSetPair |
getLowestCommonSubsumerWithLinScore(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
OwlSimMetadata |
getMetadata() |
HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> |
getMetricStats(OwlSim.Stat stat) |
protected int |
getMinimumDistanceToAncestor(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
protected int |
getMinimumDistanceViaMICA(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedSubsumers(org.semanticweb.owlapi.model.OWLClass a) |
int |
getNumSharedElements(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
protected org.semanticweb.owlapi.model.OWLClass |
getOWLClassFromShortId(String id) |
protected Set<List<org.semanticweb.owlapi.model.OWLClass>> |
getPaths(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
protected String |
getProperty(SimpleOwlSim.SimConfigurationProperty p) |
protected Boolean |
getPropertyAsBoolean(SimpleOwlSim.SimConfigurationProperty p) |
protected Double |
getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty p) |
protected Double |
getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty p,
Double dv) |
org.semanticweb.owlapi.reasoner.OWLReasoner |
getReasoner() |
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getSharedElements(org.semanticweb.owlapi.model.OWLClass c,
org.semanticweb.owlapi.model.OWLClass d) |
String |
getShortId(org.semanticweb.owlapi.model.OWLClass c) |
Properties |
getSimProperties() |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
getSimStatistics() |
SimStats |
getSimStats() |
org.semanticweb.owlapi.model.OWLOntology |
getSourceOntology() |
OwlSim.StatsPerIndividual |
getSummaryStatistics()
Fetch the pre-computed summary values
|
OwlSim.StatsPerIndividual |
getSummaryStatistics(org.semanticweb.owlapi.model.OWLClass c)
OwlSim.StatsPerIndividual summary statistic calculations using OWLClass c as the root node |
org.apache.commons.math3.stat.descriptive.SummaryStatistics |
getSummaryStatisticsForCollection(Collection<org.apache.commons.math3.stat.descriptive.SummaryStatistics> aggregate,
OwlSim.Stat stat)
This function will take an aggregated collection of Summary Statistics
and will generate a derived
SummaryStatistic based on a flag for the
desired summation. |
org.apache.commons.math3.stat.descriptive.StatisticalSummaryValues |
getSystemStats() |
boolean |
isDisableLCSCache() |
boolean |
isNoLookupForLCSCache() |
void |
precomputeAttributeAllByAll()
For implementations that use a cache, this performs an all by all comparison
of all attributes and caches the results.
|
void |
saveLCSCache(String fileName)
Saves the contents of the LCS-IC cache
Assumes that this has already been filled by comparing all classes by all classes.
|
void |
saveState(String fileName)
Experimental: save internal state of object
|
void |
setCorpusSize(int size)
Sets the number of entities in domain.
|
void |
setDisableLCSCache(boolean isDisableLCSCache)
if set, the cache is neither read nor written to.
|
void |
setEnrichmentConfig(EnrichmentConfig enrichmentConfig) |
void |
setInformationContentFromOntology(org.semanticweb.owlapi.model.OWLOntology o)
Populate the IC cache from an ontology of class-IC mappings.
|
protected abstract void |
setInformtionContectForAttribute(org.semanticweb.owlapi.model.OWLClass c,
Double v) |
void |
setNoLookupForLCSCache(boolean isNoLookupForLCSCache)
Ff set, the cache is written to but not read from.
|
void |
setSimProperties(Properties simProperties) |
void |
setSimStats(SimStats simStats) |
void |
showTimings()
Writes timing information using log4j.
|
void |
showTimingsAndReset() |
protected long |
tdelta(long prev) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
calculateCombinedScores, calculateMetricStats, compareAllAttributes, computeTFIDFMatrix, convertCountMatrixToFrequency, createElementAttributeMapFromOntology, findMatches, findMatchesWithin, getAllAttributeClasses, getAllElements, getAsymmetricAttributeJaccardSimilarity, getAsymmetricElementJaccardSimilarity, getAttributeGraphInformationContentSimilarity, getAttributeJaccardSimilarity, getAttributesForElement, getAttributeSimilarity, getCoannotatedClassesForAttribute, getCoannotatedClassesForAttribute, getCoannotatedClassesForAttribute, getCoAnnotatedClassesForAttributes, getCoAnnotatedClassesForAttributes, getCoAnnotatedClassesForIndividual, getCoAnnotatedClassesForIndividual, getCoAnnotatedClassesForMatches, getElementGraphInformationContentSimilarity, getElementJaccardSimilarity, getElementsForAttribute, getElementToAttributesMap, getGroupwiseSimilarity, getGroupwiseSimilarity, getGroupwiseSimilarity, getGroupwiseSimilarity, getGroupwiseSimilarity, getGroupwiseSimilarity, getInferredAttributes, getInformationContentForAttribute, getLowestCommonSubsumerWithIC, getLowestCommonSubsumerWithIC, getNamedCommonSubsumers, getNamedCommonSubsumers, getNamedCommonSubsumersCount, getNamedLowestCommonSubsumers, getNamedReflexiveSubsumers, getNumElementsForAttribute, getPairwiseSimilarity, getSimilarityBestMatchAverage, getSimilarityBestMatchAverageAsym, getSimilarityBestMatchAverageAsym, getSimilarityMaxIC, getSimStatistics, getSubsetCoannotationMatrix, initCoannotationMatrix, loadLCSCache, populateFullCoannotationMatrix, saveLCSCache
public SimStats simStats
protected boolean isDisableLCSCache
protected org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
protected Integer corpusSize
protected boolean isLCSCacheFullyPopulated
protected boolean isNoLookupForLCSCache
public org.apache.commons.math3.stat.descriptive.SummaryStatistics overallStats
public OwlSim.StatsPerIndividual overallSummaryStatsPerIndividual
public HashMap<org.semanticweb.owlapi.model.OWLClass,OwlSim.StatsPerIndividual> subgraphSummaryStatsPerIndividual
public org.apache.commons.math3.stat.descriptive.SummaryStatistics simStatsPerIndividual
public HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> metricStatMeans
public HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> metricStatMaxes
public HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> metricStatMins
public final String icIRIString
public EnrichmentConfig enrichmentConfig
public org.semanticweb.owlapi.model.OWLOntology getSourceOntology()
getSourceOntology
in interface OwlSim
public org.semanticweb.owlapi.reasoner.OWLReasoner getReasoner()
getReasoner
in interface OwlSim
public boolean isNoLookupForLCSCache()
public void setNoLookupForLCSCache(boolean isNoLookupForLCSCache)
OwlSim
setNoLookupForLCSCache
in interface OwlSim
public boolean isDisableLCSCache()
public void setDisableLCSCache(boolean isDisableLCSCache)
OwlSim
OwlSim.setNoLookupForLCSCache(boolean)
setDisableLCSCache
in interface OwlSim
public Properties getSimProperties()
getSimProperties
in interface OwlSim
public void setSimProperties(Properties simProperties)
setSimProperties
in interface OwlSim
public SimStats getSimStats()
getSimStats
in interface OwlSim
public void setSimStats(SimStats simStats)
protected long tdelta(long prev)
public void showTimings()
OwlSim
showTimings
in interface OwlSim
public void showTimingsAndReset()
public void precomputeAttributeAllByAll() throws UnknownOWLClassException
OwlSim
precomputeAttributeAllByAll
in interface OwlSim
UnknownOWLClassException
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedSubsumers(org.semanticweb.owlapi.model.OWLClass a)
getNamedSubsumers
in interface OwlSim
public int getCorpusSize()
OwlSim
getCorpusSize
in interface OwlSim
public void setCorpusSize(int size)
OwlSim
setCorpusSize
in interface OwlSim
protected Set<List<org.semanticweb.owlapi.model.OWLClass>> getPaths(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d)
protected int getMinimumDistanceToAncestor(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d)
protected int getMinimumDistanceViaMICA(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d) throws UnknownOWLClassException
UnknownOWLClassException
public void getICSimDisj(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d)
public OwlSim.ScoreAttributeSetPair getLowestCommonSubsumerWithLinScore(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d) throws UnknownOWLClassException
getLowestCommonSubsumerWithLinScore
in interface OwlSim
UnknownOWLClassException
public int getAttributeJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLClass a, org.semanticweb.owlapi.model.OWLClass b) throws UnknownOWLClassException
OwlSim
OwlSim.getAttributeJaccardSimilarity(OWLClass, OWLClass)
* 100getAttributeJaccardSimilarityAsPercent
in interface OwlSim
UnknownOWLClassException
public int getElementJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j) throws UnknownOWLClassException
OwlSim
OwlSim.getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual)
* 100getElementJaccardSimilarityAsPercent
in interface OwlSim
UnknownOWLClassException
public int getAsymmetricAttributeJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLClass a, org.semanticweb.owlapi.model.OWLClass b) throws UnknownOWLClassException
OwlSim
OwlSim.getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass)
* 100getAsymmetricAttributeJaccardSimilarityAsPercent
in interface OwlSim
UnknownOWLClassException
public int getAsymmetricElementJaccardSimilarityAsPercent(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j) throws UnknownOWLClassException
OwlSim
OwlSim.getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual)
* 100getAsymmetricElementJaccardSimilarityAsPercent
in interface OwlSim
UnknownOWLClassException
public Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getSharedElements(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d) throws UnknownOWLClassException
UnknownOWLClassException
public int getNumSharedElements(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d) throws UnknownOWLClassException
UnknownOWLClassException
public ElementPairScores getGroupwiseSimilarity(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j) throws Exception
OwlSim
(i,j)
.
This will default to using the following cutoffs:
minSimJPct = getPropertyAsDouble({@link SimConfigurationProperty.minimumSimJ}, 0.05) * 100)
minMaxIC = getPropertyAsDouble({@link SimConfigurationProperty.minimumMaxIC}, 2.5);
getGroupwiseSimilarity
in interface OwlSim
Exception
public List<ElementPairScores> findMatches(Set<org.semanticweb.owlapi.model.OWLClass> atts, String targetIdSpace) throws Exception
OwlSim
Find all similar matches to a pseudo-individual with a set of attributes
when compared to loaded individuals using getGroupwiseSimilarity
with default cutoffs.
minSimJPct = getPropertyAsDouble({@link SimConfigurationProperty.minimumSimJ}, 0.05) * 100)
minMaxIC = getPropertyAsDouble({@link SimConfigurationProperty.minimumMaxIC}, 2.5);
findMatches
in interface OwlSim
Exception
public List<ElementPairScores> findMatches(org.semanticweb.owlapi.model.OWLNamedIndividual i, String targetIdSpace) throws Exception
findMatches
in interface OwlSim
Exception
public List<ElementPairScores> findMatches(org.semanticweb.owlapi.model.OWLNamedIndividual i, String targetIdSpace, double minSimJPct, double minMaxIC) throws Exception
findMatches
in interface OwlSim
Exception
public Double getEntropy() throws UnknownOWLClassException
getEntropy
in interface OwlSim
UnknownOWLClassException
public Double getEntropy(Set<org.semanticweb.owlapi.model.OWLClass> cset) throws UnknownOWLClassException
getEntropy
in interface OwlSim
UnknownOWLClassException
public void dispose()
OwlSim
public org.semanticweb.owlapi.model.OWLOntology cacheInformationContentInOntology() throws org.semanticweb.owlapi.model.OWLOntologyCreationException, UnknownOWLClassException
OwlSim
cacheInformationContentInOntology
in interface OwlSim
org.semanticweb.owlapi.model.OWLOntologyCreationException
UnknownOWLClassException
protected abstract void setInformtionContectForAttribute(org.semanticweb.owlapi.model.OWLClass c, Double v)
protected abstract void clearInformationContentCache()
public void setInformationContentFromOntology(org.semanticweb.owlapi.model.OWLOntology o)
OwlSim
setInformationContentFromOntology
in interface OwlSim
public void assignDefaultInformationContentForAllClasses()
public void saveState(String fileName) throws IOException
OwlSim
saveState
in interface OwlSim
IOException
public void saveLCSCache(String fileName) throws IOException
OwlSim
saveLCSCache
in interface OwlSim
IOException
public String getShortId(org.semanticweb.owlapi.model.OWLClass c)
getShortId
in interface OwlSim
protected org.semanticweb.owlapi.model.OWLClass getOWLClassFromShortId(String id)
public EnrichmentConfig getEnrichmentConfig()
getEnrichmentConfig
in interface OwlSim
public void setEnrichmentConfig(EnrichmentConfig enrichmentConfig)
setEnrichmentConfig
in interface OwlSim
public List<EnrichmentResult> calculateAllByAllEnrichment() throws org.apache.commons.math.MathException, UnknownOWLClassException
calculateAllByAllEnrichment
in interface OwlSim
org.apache.commons.math.MathException
UnknownOWLClassException
public List<EnrichmentResult> calculateAllByAllEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass pc1, org.semanticweb.owlapi.model.OWLClass pc2) throws org.apache.commons.math.MathException, UnknownOWLClassException
OwlSim
OwlSim.calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass)
}calculateAllByAllEnrichment
in interface OwlSim
populationClass
- pc1
- - sample set root classpc2
- - enriched set root classorg.apache.commons.math.MathException
UnknownOWLClassException
public List<EnrichmentResult> filterEnrichmentResults(List<EnrichmentResult> resultsIn)
public List<EnrichmentResult> calculateEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass sampleSetClass) throws org.apache.commons.math.MathException, UnknownOWLClassException
OwlSim
calculateEnrichment
in interface OwlSim
populationClass
- sampleSetClass
- org.apache.commons.math.MathException
UnknownOWLClassException
public EnrichmentResult calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass sampleSetClass, org.semanticweb.owlapi.model.OWLClass enrichedClass) throws org.apache.commons.math.MathException, UnknownOWLClassException
OwlSim
calculatePairwiseEnrichment
in interface OwlSim
populationClass
- sampleSetClass
- enrichedClass
- org.apache.commons.math.MathException
UnknownOWLClassException
public double getConditionalProbability(org.semanticweb.owlapi.model.OWLClass c, org.semanticweb.owlapi.model.OWLClass d) throws UnknownOWLClassException
getConditionalProbability
in interface OwlSim
c
- d
- UnknownOWLClassException
protected String getProperty(SimpleOwlSim.SimConfigurationProperty p)
protected Double getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty p)
protected Double getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty p, Double dv)
protected Boolean getPropertyAsBoolean(SimpleOwlSim.SimConfigurationProperty p)
public void computeSystemStats() throws UnknownOWLClassException
OwlSim
computeSystemStats
in interface OwlSim
UnknownOWLClassException
public void computeSystemStatsForSubgraph(org.semanticweb.owlapi.model.OWLClass c) throws UnknownOWLClassException
computeSystemStatsForSubgraph
in interface OwlSim
UnknownOWLClassException
public org.apache.commons.math3.stat.descriptive.SummaryStatistics getSummaryStatisticsForCollection(Collection<org.apache.commons.math3.stat.descriptive.SummaryStatistics> aggregate, OwlSim.Stat stat)
SummaryStatistic
based on a flag for the
desired summation. This is particularly helpful for finding out the
means of the individual statistics of the collection.
For example, if you wanted to find out the mean of means of the collection
you would call this function like getSummaryStatisticsForCollection(aggregate,1).getMean();
Or if you wanted to determine the max number of annotations per individual, you could call:
getSummaryStatisticsForCollection(aggregate,5).getMax();
The stat flag should be set to the particular individual statistic that should be summarized over.
aggregate
- The aggregated collection of summary statisticsstat
- Integer flag for the statistic (1:mean ; 2:sum; 3:min; 4:max; 5:N)SummaryStatistics
of the selected statisticpublic org.apache.commons.math3.stat.descriptive.SummaryStatistics computeIndividualStats(org.semanticweb.owlapi.model.OWLNamedIndividual i) throws UnknownOWLClassException
OwlSim
computeIndividualStats
in interface OwlSim
UnknownOWLClassException
public org.apache.commons.math3.stat.descriptive.SummaryStatistics computeIndividualStatsForSubgraph(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c) throws UnknownOWLClassException
UnknownOWLClassException
public org.apache.commons.math3.stat.descriptive.SummaryStatistics computeAttributeSetSimilarityStats(Set<org.semanticweb.owlapi.model.OWLClass> atts)
computeAttributeSetSimilarityStats
in interface OwlSim
public org.apache.commons.math3.stat.descriptive.SummaryStatistics computeAttributeSetSimilarityStatsForSubgraph(Set<org.semanticweb.owlapi.model.OWLClass> atts, org.semanticweb.owlapi.model.OWLClass sub)
computeAttributeSetSimilarityStatsForSubgraph
in interface OwlSim
public org.apache.commons.math3.stat.descriptive.StatisticalSummaryValues getSystemStats()
getSystemStats
in interface OwlSim
public OwlSim.StatsPerIndividual getSummaryStatistics()
OwlSim
getSummaryStatistics
in interface OwlSim
SummaryStatistics
public OwlSim.StatsPerIndividual getSummaryStatistics(org.semanticweb.owlapi.model.OWLClass c)
OwlSim
OwlSim.StatsPerIndividual
summary statistic calculations using OWLClass
c as the root nodegetSummaryStatistics
in interface OwlSim
c
- OWLClass
OwlSim.StatsPerIndividual
public org.apache.commons.math3.stat.descriptive.SummaryStatistics getSimStatistics()
public org.apache.commons.math3.stat.descriptive.SummaryStatistics computeIndividualSimilarityStats(org.semanticweb.owlapi.model.OWLNamedIndividual i) throws UnknownOWLClassException
UnknownOWLClassException
public HashMap<String,org.apache.commons.math3.stat.descriptive.SummaryStatistics> getMetricStats(OwlSim.Stat stat)
getMetricStats
in interface OwlSim
public double calculateOverallAnnotationSufficiencyForIndividual(org.semanticweb.owlapi.model.OWLNamedIndividual i) throws UnknownOWLClassException
calculateOverallAnnotationSufficiencyForIndividual
in interface OwlSim
UnknownOWLClassException
public double calculateSubgraphAnnotationSufficiencyForIndividual(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c) throws UnknownOWLClassException
UnknownOWLClassException
public double calculateOverallAnnotationSufficiencyForAttributeSet(Set<org.semanticweb.owlapi.model.OWLClass> atts) throws UnknownOWLClassException
calculateOverallAnnotationSufficiencyForAttributeSet
in interface OwlSim
UnknownOWLClassException
public double calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<org.semanticweb.owlapi.model.OWLClass> atts, org.semanticweb.owlapi.model.OWLClass c) throws UnknownOWLClassException
calculateSubgraphAnnotationSufficiencyForAttributeSet
in interface OwlSim
UnknownOWLClassException
public void calculateCombinedScore(ElementPairScores s, double maxMaxIC, double maxBMA)
calculateCombinedScore
in interface OwlSim
public OwlSimMetadata getMetadata()
getMetadata
in interface OwlSim
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