…ple boolean limit case

of other matchers; e.g. jaccard with a floor function.

although this is not anticipated to be useful for the general phenotype search use case,
it can be useful to leverage owlsim services for doing basic queries of the form:
find all genes with phenotypes A and B but not C

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcher.java

@@ -27,8 +27,8 @@ public ClassMatcher(BMKnowledgeBase kb) {
 	/**
 	 * Find best match for every class in ont1, where the best match is in ont2
 	 * 
-	 * @param qOnt
-	 * @param tOnt
+	 * @param qOnt - ontology prefix
+	 * @param tOnt - ontology prefix
 	 * @return list of matches
 	 */
 	public List<SimpleClassMatch> matchOntologies(String qOnt, String tOnt) {
@@ -37,8 +37,17 @@ public ClassMatcher(BMKnowledgeBase kb) {
 		return matchClassSets(qids, tids);
 	}
 
+	/**
+	 * Find best matches for all class combos {qid1, ...} x {tid1, ...}
+	 * 
+	 * @param qids - classes
+	 * @param tids - classes
+	 * @return list of matches
+	 */
 	public List<SimpleClassMatch> matchClassSets(Set<String> qids, Set<String> tids) {
 		ArrayList<SimpleClassMatch> matches = new ArrayList<>();
+		
+		// TODO: consider optimization, by first grouping by system
 		for (String q : qids) {
 			matches.add(getBestMatch(q, tids));
 		}
@@ -58,6 +67,8 @@ private SimpleClassMatch getBestMatch(String q, Set<String> tids) {
 				bestEqScore = eqScore;
 				best = t;
 			}
+			if (bestEqScore >= 1.0)
+			    break;
 		}
 
 		EWAHCompressedBitmap tbm = kb.getSuperClassesBM(best);

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

@@ -0,0 +1,90 @@
+package org.monarchinitiative.owlsim.compute.matcher.impl;
+
+import java.util.List;
+
+import javax.inject.Inject;
+
+import org.apache.log4j.Logger;
+import org.monarchinitiative.owlsim.compute.matcher.NegationAwareProfileMatcher;
+import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.monarchinitiative.owlsim.kb.filter.UnknownFilterException;
+import org.monarchinitiative.owlsim.model.match.MatchSet;
+import org.monarchinitiative.owlsim.model.match.ProfileQuery;
+import org.monarchinitiative.owlsim.model.match.QueryWithNegation;
+import org.monarchinitiative.owlsim.model.match.impl.MatchSetImpl;
+
+import com.googlecode.javaewah.EWAHCompressedBitmap;
+
+/**
+ * Implements a standard boolean query
+ * 
+ * @author cjm
+ *
+ */
+public class BooleanProfileMatcher extends AbstractProfileMatcher implements NegationAwareProfileMatcher {
+	
+	private Logger LOG = Logger.getLogger(BooleanProfileMatcher.class);
+	
+	/**
+	 * @param kb
+	 */
+	@Inject
+	public BooleanProfileMatcher(BMKnowledgeBase kb) {
+		super(kb);
+	}
+	
+
+	/**
+	 * @param kb
+	 * @return new instance
+	 */
+	public static ProfileMatcher create(BMKnowledgeBase kb) {
+		return new BooleanProfileMatcher(kb);
+	}
+
+	@Override
+	public String getShortName() {
+		return "boolean";
+	}
+
+	/**
+	 * @param q
+	 * @return match profile containing probabilities of each individual
+	 * @throws UnknownFilterException 
+	 */
+	public MatchSet findMatchProfileImpl(ProfileQuery q) throws UnknownFilterException {
+		
+		EWAHCompressedBitmap queryProfileBM = getDirectProfileBM(q);
+        boolean hasNegationQuery = false;
+        EWAHCompressedBitmap negatedQueryProfileBM = null;
+        if (q instanceof QueryWithNegation) {
+            negatedQueryProfileBM = getDirectNegatedProfileBM((QueryWithNegation) q);
+            hasNegationQuery = negatedQueryProfileBM.cardinality() > 0;
+        }
+
+		// TODO
+		MatchSet mp =  MatchSetImpl.create(q);
+		int qcard = queryProfileBM.cardinality();
+		List<String> indIds = getFilteredIndividualIds(q.getFilter());
+		for (String itemId : indIds) {
+			EWAHCompressedBitmap targetProfileBM = knowledgeBase.getTypesBM(itemId);
+			int numInQueryAndInTarget = queryProfileBM.andCardinality(targetProfileBM);
+			if (numInQueryAndInTarget == qcard) {
+			    if (!hasNegationQuery ||
+			            negatedQueryProfileBM.andCardinality(targetProfileBM) == 0) {
+		            String label = knowledgeBase.getLabelMapper().getArbitraryLabel(itemId);
+		            mp.add(createMatch(itemId, label, 1));
+			        
+			    }
+			}
+		}
+		mp.sortMatches();
+		return mp;
+	}
+
+
+
+
+
+}

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/ProfileMatchEvaluator.java

@@ -78,6 +78,8 @@ public boolean evaluateTestQuery(ProfileMatcher profileMatcher, TestQuery tq) th
 
 		if (jsonWriter != null) {
 			LOG.info("Writing MatchSet using "+jsonWriter+" results will appear in "+jsonWriter);
+			jsonWriter.write(mp.getMatches().get(0));
+			LOG.info("MATCHES:"+mp);
 			jsonWriter.write(mp);
 		}
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/TestQuery.java

@@ -27,4 +27,14 @@ public TestQuery(ProfileQuery query, String expectedId, int maxRank) {
 		this.expectedId = expectedId;
 		this.maxRank = maxRank;
 	}
+    /* (non-Javadoc)
+     * @see java.lang.Object#toString()
+     */
+    @Override
+    public String toString() {
+        return "TestQuery [query=" + query + ", expectedId=" + expectedId
+                + ", maxRank=" + maxRank + ", matchSet=" + matchSet + "]";
+    }
+	
+	
 }

owlsim-core/src/main/java/org/monarchinitiative/owlsim/model/match/impl/MatchSetImpl.java

@@ -23,7 +23,8 @@
  *
  */
 public class MatchSetImpl implements MatchSet {
-	private ProfileQuery query;
+
+    private ProfileQuery query;
 	private List<Match> matches; // TODO - make this neutral
 	ExecutionMetadata executionMetadata;
 	MethodMetadata methodMetadata;
@@ -210,8 +211,10 @@ public String toString() {
 
 	public void calculateMatchSignificance(DescriptiveStatistics background) {
 		for (Match m : this.matches) {
-			double p = TestUtils.tTest(m.getScore(), background);
-			m.setSignificance(p);
+		    if (background.getN() > 1) { 
+		        double p = TestUtils.tTest(m.getScore(), background);
+		        m.setSignificance(p);
+		    }
 		}
 	}
 

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/AbstractProfileMatcherTest.java

@@ -192,6 +192,17 @@ protected boolean isRankedLast(String matchId, MatchSet matchSet) {
 		return true;
 	}
 	
+	protected boolean isNotInMatchSet(String matchId, MatchSet matchSet) {
+	    for (Match m : matchSet.getMatches()) {
+	        if (m.getMatchId().equals(matchId)) {
+	           return false;
+	        }
+	    }
+	    return true;
+	}
+
+
+	
 	protected boolean isRankedAt(String matchId, MatchSet matchSet, int expectedRank) {
 	    int matchRank = 0;
 	    for (Match m : matchSet.getMatches()) {

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/BooleanProfileMatcherTest.java

@@ -0,0 +1,73 @@
+package org.monarchinitiative.owlsim.compute.matcher;
+
+import org.apache.log4j.Logger;
+import org.junit.Assert;
+import org.junit.Test;
+import org.monarchinitiative.owlsim.compute.matcher.impl.BooleanProfileMatcher;
+import org.monarchinitiative.owlsim.eval.TestQuery;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.monarchinitiative.owlsim.model.match.ProfileQuery;
+
+public class BooleanProfileMatcherTest extends AbstractProfileMatcherTest {
+
+    private Logger LOG = Logger.getLogger(BooleanProfileMatcherTest.class);
+
+    protected ProfileMatcher createProfileMatcher(BMKnowledgeBase kb) {
+        return BooleanProfileMatcher.create(kb);
+    }
+    @Test
+    public void testBoolean() throws Exception {
+        loadSimplePhenoWithNegation();
+        //LOG.info("INDS="+kb.getIndividualIdsInSignature());
+        ProfileMatcher profileMatcher = createProfileMatcher(kb);
+
+        int nOk = 0;
+        for (String i : kb.getIndividualIdsInSignature()) {
+            LOG.info("I: "+i);
+            if (i.equals("http://x.org/ind-no-brain-phenotype")) {
+                continue;
+            }
+            if (i.equals("http://x.org/ind-unstated-phenotype")) {
+                continue;
+            }
+            ProfileQuery pq = profileMatcher.createProfileQuery(i);
+            TestQuery tq =  new TestQuery(pq, i, 1); // self should always be ranked first
+            String fn = i.replaceAll(".*/", "");
+            eval.writeJsonTo("target/boolean-test-results-"+fn+".json");
+            
+            LOG.info("Evaluating for "+i);
+            eval.evaluateTestQuery(profileMatcher, tq);
+            //Assert.assertTrue(eval.evaluateTestQuery(profileMatcher, tq));
+
+            if (i.equals("http://x.org/ind-dec-all")) {
+                Assert.assertTrue(isNotInMatchSet("http://x.org/ind-unstated-phenotype", tq.matchSet));
+                nOk++;
+            }
+            if (i.equals("http://x.org/ind-small-heart-big-brain")) {
+                Assert.assertTrue(isNotInMatchSet("http://x.org/ind-bone", tq.matchSet));
+                nOk++;
+            }
+
+        }
+        Assert.assertEquals(2, nOk);
+    }
+    
+    @Test
+    public void testExampleWithNegation() throws Exception {
+        loadSimplePhenoWithNegation();
+        //LOG.info("INDS="+kb.getIndividualIdsInSignature());
+        ProfileMatcher profileMatcher = createProfileMatcher(kb);
+
+        int nOk = 0;
+        String i = "http://x.org/ind-small-heart-big-brain";
+
+        ProfileQuery pq = profileMatcher.createProfileQuery(i);
+        TestQuery tq =  new TestQuery(pq, i, 1); // self should always be ranked first
+        String fn = i.replaceAll(".*/", "");
+        eval.writeJsonTo("target/boolean-extra-test-results-"+fn+".json");
+        Assert.assertTrue(eval.evaluateTestQuery(profileMatcher, tq));
+        
+        Assert.assertTrue(isNotInMatchSet("http://x.org/ind-no-brain-phenotype", tq.matchSet));
+
+    }
+}