[#62] we still need the the inject indicator for guice. We can the ma…

…tcher package through java reflection and let the injector construct the objects.

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/ProfileMatcher.java

@@ -111,6 +111,4 @@ public ProfileQuery createProfileQueryFromClasses(Set<String> classIds,
 	 */
 	BMKnowledgeBase getKnowledgeBase();
 
-
-
 }

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;

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();

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);
 	}

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);
 	}

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);
 	}

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);
 	}

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);
     }

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);
 	}

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<Integer,Map<Integer,WeightedTypesBM>> individualToInterpretationToTypesBM = new HashMap<>();
 
+    @Inject
 	protected NaiveBayesFixedWeightTwoStateProfileMatcher(BMKnowledgeBase kb) {
 		super(kb);
 	}

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);
 	}

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);
 	}

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<BitMapPair,NodeProbabilities[]> targetToQueryCache;
 
+    @Inject
 	private ThreeStateBayesianNetworkProfileMatcher(BMKnowledgeBase kb) {
 		super(kb);
 	}

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);
+	}
 
 }