diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/ProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/ProfileMatcher.java index 52b58cb..a710112 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/ProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/ProfileMatcher.java @@ -111,6 +111,4 @@ public ProfileQuery createProfileQueryFromClasses(Set classIds, */ BMKnowledgeBase getKnowledgeBase(); - - } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/AbstractSemanticSimilarityProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/AbstractSemanticSimilarityProfileMatcher.java index eb042fa..0b8f0ca 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/AbstractSemanticSimilarityProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/AbstractSemanticSimilarityProfileMatcher.java @@ -1,5 +1,7 @@ package org.monarchinitiative.owlsim.compute.matcher.impl; +import javax.inject.Inject; + import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator; import org.monarchinitiative.owlsim.compute.mica.impl.MostInformativeCommonAncestorCalculatorImpl; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java index ee22a60..580dd3b 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java @@ -5,6 +5,8 @@ import java.util.Map; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.cpt.ConditionalProbabilityIndex; import org.monarchinitiative.owlsim.compute.cpt.IncoherentStateException; @@ -101,6 +103,7 @@ private Calculator[] calculatorCache; private Double[][] targetClassProbabilityCache; + @Inject private BayesianNetworkProfileMatcher(BMKnowledgeBase kb) { super(kb); int N = kb.getIndividualIdsInSignature().size(); diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridNegatedProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridNegatedProfileMatcher.java index 04b85c3..0a693e4 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridNegatedProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridNegatedProfileMatcher.java @@ -1,5 +1,7 @@ package org.monarchinitiative.owlsim.compute.matcher.impl; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.NegationAwareProfileMatcher; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; @@ -22,6 +24,7 @@ /** * @param kb */ + @Inject public GridNegatedProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridProfileMatcher.java index c2f4448..499f58e 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/GridProfileMatcher.java @@ -3,6 +3,8 @@ import java.util.List; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator.ClassInformationContentPair; @@ -32,6 +34,7 @@ /** * @param kb */ + @Inject public GridProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/JaccardSimilarityProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/JaccardSimilarityProfileMatcher.java index cdca4a7..a589c89 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/JaccardSimilarityProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/JaccardSimilarityProfileMatcher.java @@ -2,6 +2,8 @@ import java.util.List; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; @@ -26,6 +28,7 @@ /** * @param kb */ + @Inject public JaccardSimilarityProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/MaximumInformationContentSimilarityProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/MaximumInformationContentSimilarityProfileMatcher.java index c14bec9..a1f59ce 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/MaximumInformationContentSimilarityProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/MaximumInformationContentSimilarityProfileMatcher.java @@ -2,6 +2,8 @@ import java.util.List; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator.ClassInformationContentPair; @@ -28,6 +30,7 @@ /** * @param kb */ + @Inject private MaximumInformationContentSimilarityProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightThreeStateProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightThreeStateProfileMatcher.java index bb3b7d2..7f13bc0 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightThreeStateProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightThreeStateProfileMatcher.java @@ -4,6 +4,8 @@ import java.util.List; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.NegationAwareProfileMatcher; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; @@ -29,6 +31,7 @@ private Logger LOG = Logger.getLogger(NaiveBayesFixedWeightThreeStateProfileMatcher.class); + @Inject private NaiveBayesFixedWeightThreeStateProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher.java index 009b47c..1518072 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher.java @@ -1,5 +1,7 @@ package org.monarchinitiative.owlsim.compute.matcher.impl; +import javax.inject.Inject; + import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; /** @@ -8,6 +10,7 @@ */ public class NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher extends NaiveBayesFixedWeightTwoStateProfileMatcher { + @Inject private NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateProfileMatcher.java index 392a021..31fbc80 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesFixedWeightTwoStateProfileMatcher.java @@ -7,6 +7,8 @@ import java.util.Map; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; @@ -76,6 +78,7 @@ public WeightedTypesBM(EWAHCompressedBitmap typesBM, Double weight) { // for maps a pair of (Individual, InterpretationIndex) to a set of inferred (self, direct, indirect) types private Map> individualToInterpretationToTypesBM = new HashMap<>(); + @Inject protected NaiveBayesFixedWeightTwoStateProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesVariableWeightProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesVariableWeightProfileMatcher.java index a06d0ac..8084cc0 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesVariableWeightProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/NaiveBayesVariableWeightProfileMatcher.java @@ -3,6 +3,8 @@ import java.util.List; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; @@ -34,6 +36,7 @@ /** * @param kb */ + @Inject public NaiveBayesVariableWeightProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/PhenodigmICProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/PhenodigmICProfileMatcher.java index 8d3f8f0..62489a6 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/PhenodigmICProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/PhenodigmICProfileMatcher.java @@ -3,6 +3,8 @@ import java.util.List; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher; import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator.ClassInformationContentPair; @@ -32,6 +34,7 @@ /** * @param kb */ + @Inject public PhenodigmICProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java index 2efe966..e7c207d 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/ThreeStateBayesianNetworkProfileMatcher.java @@ -6,6 +6,8 @@ import java.util.Map; import java.util.Set; +import javax.inject.Inject; + import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.compute.cpt.IncoherentStateException; import org.monarchinitiative.owlsim.compute.cpt.impl.NodeProbabilities; @@ -35,6 +37,7 @@ private ThreeStateConditionalProbabilityIndex cpi = null; private Map targetToQueryCache; + @Inject private ThreeStateBayesianNetworkProfileMatcher(BMKnowledgeBase kb) { super(kb); } diff --git a/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java b/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java index 429aa97..e6b76c7 100644 --- a/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java +++ b/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java @@ -14,6 +14,11 @@ import javax.inject.Singleton; import org.apache.commons.validator.routines.UrlValidator; +import org.monarchinitiative.owlsim.compute.classmatch.ClassMatcher; +import org.monarchinitiative.owlsim.compute.enrich.impl.HypergeometricEnrichmentEngine; +import org.monarchinitiative.owlsim.compute.matcher.impl.BayesianNetworkProfileMatcher; +import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator; +import org.monarchinitiative.owlsim.compute.mica.impl.MostInformativeCommonAncestorCalculatorImpl; import org.monarchinitiative.owlsim.kb.BMKnowledgeBase; import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl; import org.monarchinitiative.owlsim.services.modules.bindings.IndicatesDataTsvs; @@ -123,5 +128,25 @@ OWLOntology getDataTsvs(OWLOntologyManager manager) throws OWLOntologyCreationException, FileNotFoundException, IOException { return mergeOntologies(manager, dataTsvs); } + + @Provides + MostInformativeCommonAncestorCalculator getMostInformativeCommonAncestorCalculator(BMKnowledgeBase knowledgeBase) { + return new MostInformativeCommonAncestorCalculatorImpl(knowledgeBase); + } + + @Provides + HypergeometricEnrichmentEngine getHypergeometricEnrichmentEngine(BMKnowledgeBase knowledgeBase) { + return new HypergeometricEnrichmentEngine(knowledgeBase); + } + + @Provides + BayesianNetworkProfileMatcher getBayesianNetworkProfileMatcher(BMKnowledgeBase knowledgeBase) { + return BayesianNetworkProfileMatcher.create(knowledgeBase); + } + + @Provides + ClassMatcher getClassMatcher(BMKnowledgeBase knowledgeBase) { + return new ClassMatcher(knowledgeBase); + } }