Merge pull request #49 from monarch-initiative/fix_typo_methodname

change method-name converIndexSetToBitmap to convertIndexSetToBitmap

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/enrich/impl/HypergeometricEnrichmentEngine.java

@@ -230,7 +230,7 @@ protected EWAHCompressedBitmap getIndividualsBM(EnrichmentQuery q) {
             return kb.getIndividualsBM(q.getClassId());
         else if (q.getIndividualIds() != null) {
             Set<Integer> ixs = q.getIndividualIds().stream().map( x -> kb.getIndividualIndex(x)).collect(Collectors.toSet());
-            return EWAHUtils.converIndexSetToBitmap(ixs);
+            return EWAHUtils.convertIndexSetToBitmap(ixs);
         }
         else {
             return null;

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

@@ -86,7 +86,7 @@ protected EWAHCompressedBitmap getDirectProfileBM(ProfileQuery q) {
         for (String cid : q.getQueryClassIds()) {
             positions.add(knowledgeBase.getClassIndex(cid));
         }
-        return EWAHUtils.converIndexSetToBitmap(positions);
+        return EWAHUtils.convertIndexSetToBitmap(positions);
     }
 
     // given an array of class IDs c1...cn, return an array S1...Sn,
@@ -114,7 +114,7 @@ protected EWAHCompressedBitmap getNegatedProfileBM(ProfileQuery q) {
             int ci = knowledgeBase.getClassIndex(id);
             bits.addAll( knowledgeBase.getSubClasses(ci).getPositions() );
         }
-        return EWAHUtils.converIndexSetToBitmap(bits);
+        return EWAHUtils.convertIndexSetToBitmap(bits);
     }
 
     protected EWAHCompressedBitmap getDirectNegatedProfileBM(QueryWithNegation q) {
@@ -124,7 +124,7 @@ protected EWAHCompressedBitmap getDirectNegatedProfileBM(QueryWithNegation q) {
             int ci = knowledgeBase.getClassIndex(id);
             bits.add(ci);
         }
-        return EWAHUtils.converIndexSetToBitmap(bits);
+        return EWAHUtils.convertIndexSetToBitmap(bits);
     }
 
     protected Match createMatch(String matchId, String matchLabel, double s) {

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

@@ -64,7 +64,7 @@ private EWAHCompressedBitmap getQueryBlanketBM(ProfileQuery q) {
 			}
 		}
 
-		return onQueryNodesBM.or(EWAHUtils.converIndexSetToBitmap(nodesWithOnParents));
+		return onQueryNodesBM.or(EWAHUtils.convertIndexSetToBitmap(nodesWithOnParents));
 	}
 
 	// any negated query node that has at least one negated parent;
@@ -82,7 +82,7 @@ private EWAHCompressedBitmap getQueryNegatedNoTransition(EWAHCompressedBitmap ne
 			}
 		}
 
-		return EWAHUtils.converIndexSetToBitmap(nodes);
+		return EWAHUtils.convertIndexSetToBitmap(nodes);
 	}
 
 
@@ -148,10 +148,10 @@ public MatchSet findMatchProfileImpl(ProfileQuery q) {
 			}
 
 		}
-		EWAHCompressedBitmap nodesQuPtBM = EWAHUtils.converIndexSetToBitmap(nodesQuPt);
-		EWAHCompressedBitmap nodesQuPuBM = EWAHUtils.converIndexSetToBitmap(nodesQuPu);
-		EWAHCompressedBitmap nodesQfPtBM = EWAHUtils.converIndexSetToBitmap(nodesQfPtu);
-		EWAHCompressedBitmap nodesQfPuBM = EWAHUtils.converIndexSetToBitmap(nodesQfPu);
+		EWAHCompressedBitmap nodesQuPtBM = EWAHUtils.convertIndexSetToBitmap(nodesQuPt);
+		EWAHCompressedBitmap nodesQuPuBM = EWAHUtils.convertIndexSetToBitmap(nodesQuPu);
+		EWAHCompressedBitmap nodesQfPtBM = EWAHUtils.convertIndexSetToBitmap(nodesQfPtu);
+		EWAHCompressedBitmap nodesQfPuBM = EWAHUtils.convertIndexSetToBitmap(nodesQfPu);
 
 
 		// include subclasses

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

@@ -97,7 +97,7 @@ private EWAHCompressedBitmap getQueryBlanketBM(ProfileQuery q) {
 			}
 		}
 
-		return onQueryNodesBM.or(EWAHUtils.converIndexSetToBitmap(nodesWithOnParents));
+		return onQueryNodesBM.or(EWAHUtils.convertIndexSetToBitmap(nodesWithOnParents));
 	}
 
 	/**

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/stats/ICStatsCalculator.java

@@ -205,7 +205,7 @@ private EWAHCompressedBitmap getDirectProfileBM(Set<String> classIds) {
 		for (String cid : classIds) {
 			positions.add(knowledgeBase.getClassIndex(cid));
 		}
-		return EWAHUtils.converIndexSetToBitmap(positions);
+		return EWAHUtils.convertIndexSetToBitmap(positions);
 	}
 
 }

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/BackgroundData.java

@@ -74,7 +74,7 @@ public EWAHCompressedBitmap[] createRandom(int n) {
 			for (int j=0; j<setLength; j++) {
 				ibits.add(rand.nextInt(max));
 			}
-			bm = EWAHUtils.converIndexSetToBitmap(ibits);
+			bm = EWAHUtils.convertIndexSetToBitmap(ibits);
 //			LOG.info("Created random set with length "+setLength);
 			newbms[i] = bm;
 		}		
@@ -118,7 +118,7 @@ public EWAHCompressedBitmap[] createRandomWeightedByInstances(int n) {
 			for (int j=0; j<setLength; j++) {
 				ibits.add(allClasses.get(rand.nextInt(max)));
 			}
-			bm = EWAHUtils.converIndexSetToBitmap(ibits);
+			bm = EWAHUtils.convertIndexSetToBitmap(ibits);
 //			LOG.info("Created random set with length "+setLength);
 			newbms[i] = bm;
 		}				

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/LiftAllSimulatedData.java

@@ -41,7 +41,7 @@ public EWAHCompressedBitmap[] createAttributeSets(EWAHCompressedBitmap atts)
 			throws Exception {
 
 		int thing = this.getKnowledgeBase().getRootIndex(); //is this OWL:Thing?
-		EWAHCompressedBitmap thingBM = EWAHUtils.converIndexSetToBitmap(new HashSet<Integer>(thing));
+		EWAHCompressedBitmap thingBM = EWAHUtils.convertIndexSetToBitmap(new HashSet<Integer>(thing));
 
 		EWAHCompressedBitmap liftAll = new EWAHCompressedBitmap();
 		EWAHCompressedBitmap[] attrSets = new EWAHCompressedBitmap[numLevels];

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/LiftOneSimulatedData.java

@@ -41,7 +41,7 @@ public EWAHCompressedBitmap[] createAttributeSets(EWAHCompressedBitmap atts)
 	private EWAHCompressedBitmap[] createAttributeSetsRecursive(EWAHCompressedBitmap atts, EWAHCompressedBitmap[] derivedAtts) {
 
 		int thing = this.getKnowledgeBase().getRootIndex(); //is this OWL:Thing?
-		EWAHCompressedBitmap thingBM = EWAHUtils.converIndexSetToBitmap(new HashSet<Integer>(thing));
+		EWAHCompressedBitmap thingBM = EWAHUtils.convertIndexSetToBitmap(new HashSet<Integer>(thing));
 		EWAHCompressedBitmap[] attrSets = new EWAHCompressedBitmap[atts.cardinality()];
 
 		List<Integer> aList = atts.getPositions();

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RandomChooseNSimulatedData.java

@@ -97,7 +97,7 @@ private EWAHCompressedBitmap[] makeSetofRandomSubsets(EWAHCompressedBitmap atts)
 		//do this in a while loop instead of for loop
 		while ((subsetCounter < numSets) ) { //&& (subsetTries < 7*maxNumSets)
 			Set<Integer> randomSet = makeRandomSubset(atts, setLength);
-			sets.add(EWAHUtils.converIndexSetToBitmap(randomSet));
+			sets.add(EWAHUtils.convertIndexSetToBitmap(randomSet));
 //			LOG.info("Set size="+sets.size());
 			subsetCounter++;
 		}

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RemoveByCategorySimulatedData.java

@@ -232,7 +232,7 @@ public EWAHCompressedBitmap[] createAttributeSets(EWAHCompressedBitmap atts)
 					j++;
 				}
 				//make BM from set
-				bm = EWAHUtils.converIndexSetToBitmap(s);
+				bm = EWAHUtils.convertIndexSetToBitmap(s);
 				double finalSumIC= calc.getICStatsForAttributesByBM(bm).getSum();
 				LOG.info("finalIC= "+(finalSumIC)+" targetIC="+(sumIC-categorySumIC)+" removed |n|="+(atts.cardinality()-bm.cardinality()));
 				if (bm.cardinality() > 0) {

owlsim-core/src/main/java/org/monarchinitiative/owlsim/eval/data/RemoveByICThresholdSimulatedData.java

@@ -62,7 +62,7 @@ public EWAHCompressedBitmap[] createAttributeSets(EWAHCompressedBitmap atts)
 			}
 		}
 		if (s.size() > 0) {
-			attrSets[0] = EWAHUtils.converIndexSetToBitmap(s);
+			attrSets[0] = EWAHUtils.convertIndexSetToBitmap(s);
 		}
 
 		return attrSets;

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/ewah/EWAHKnowledgeBaseStore.java

@@ -216,7 +216,7 @@ public EWAHCompressedBitmap getDirectTypes(int individualIndex, int classIndex)
 	 * @return all classes directly instantiated by individual, that are subclasses of classIndex
 	 */
 	public EWAHCompressedBitmap getDirectTypes(Set<Integer> clsIndices, int classIndex) {
-		EWAHCompressedBitmap bm = EWAHUtils.converIndexSetToBitmap(clsIndices);
+		EWAHCompressedBitmap bm = EWAHUtils.convertIndexSetToBitmap(clsIndices);
 		EWAHCompressedBitmap subclasses = getSubClasses(classIndex);
 		return bm.and(subclasses);
 	}
@@ -267,7 +267,7 @@ public EWAHCompressedBitmap getDirectIndividuals(int classIndex) {
 	 * @param superClasses
 	 */
 	public void setSuperClasses(int clsIndex, Set<Integer> superClasses) {
-		 storedSuperClasses[clsIndex] = EWAHUtils.converIndexSetToBitmap(superClasses);
+		 storedSuperClasses[clsIndex] = EWAHUtils.convertIndexSetToBitmap(superClasses);
 	}
 
 	/**
@@ -278,7 +278,7 @@ public void setSuperClasses(int clsIndex, Set<Integer> superClasses) {
 	 * @param superClasses
 	 */
 	public void setDirectSuperClasses(int clsIndex, Set<Integer> superClasses) {
-		 storedDirectSuperClasses[clsIndex] = EWAHUtils.converIndexSetToBitmap(superClasses);
+		 storedDirectSuperClasses[clsIndex] = EWAHUtils.convertIndexSetToBitmap(superClasses);
 	}
 
 
@@ -304,7 +304,7 @@ public void setStoredDirectSubClasses(
 	 */
 	public void setDirectSubClasses(int clsIndex,
 			Set<Integer> subClasses) {
-		storedDirectSubClasses[clsIndex] = EWAHUtils.converIndexSetToBitmap(subClasses);
+		storedDirectSubClasses[clsIndex] = EWAHUtils.convertIndexSetToBitmap(subClasses);
 	}
 
 	/**
@@ -313,7 +313,7 @@ public void setDirectSubClasses(int clsIndex,
 	 */
 	public void setSubClasses(int clsIndex,
 			Set<Integer> subClasses) {
-		storedSubClasses[clsIndex] = EWAHUtils.converIndexSetToBitmap(subClasses);
+		storedSubClasses[clsIndex] = EWAHUtils.convertIndexSetToBitmap(subClasses);
 	}
 
 
@@ -327,7 +327,7 @@ public void setSubClasses(int clsIndex,
 	 * @param types 
 	 */
 	public void setTypes(int individualIndex, Set<Integer> types) {
-		 storedTypes[individualIndex] = EWAHUtils.converIndexSetToBitmap(types);
+		 storedTypes[individualIndex] = EWAHUtils.convertIndexSetToBitmap(types);
 	}
 
 	/**
@@ -339,23 +339,23 @@ public void setTypes(int individualIndex, Set<Integer> types) {
 	 * @param types 
 	 */
 	public void setDirectTypes(int individualIndex, Set<Integer> types) {
-		 storedDirectTypes[individualIndex] = EWAHUtils.converIndexSetToBitmap(types);
+		 storedDirectTypes[individualIndex] = EWAHUtils.convertIndexSetToBitmap(types);
 	}
 
 	/**
 	 * @param individualIndex
 	 * @param types
 	 */
 	public void setNegatedTypes(int individualIndex, Set<Integer> types) {
-		 storedNegatedTypes[individualIndex] = EWAHUtils.converIndexSetToBitmap(types);
+		 storedNegatedTypes[individualIndex] = EWAHUtils.convertIndexSetToBitmap(types);
 	}
 
 	/**
 	 * @param individualIndex
 	 * @param types
 	 */
 	public void setDirectNegatedTypes(int individualIndex, Set<Integer> types) {
-		 storedDirectNegatedTypes[individualIndex] = EWAHUtils.converIndexSetToBitmap(types);
+		 storedDirectNegatedTypes[individualIndex] = EWAHUtils.convertIndexSetToBitmap(types);
 	}
 
 
@@ -370,7 +370,7 @@ public void setDirectNegatedTypes(int individualIndex, Set<Integer> types) {
 	 * @param individuals
 	 */
 	public void setDirectIndividuals(int classIndex, Set<Integer> individuals) {
-		storedDirectIndividuals[classIndex] = EWAHUtils.converIndexSetToBitmap(individuals);
+		storedDirectIndividuals[classIndex] = EWAHUtils.convertIndexSetToBitmap(individuals);
 	}
 
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/ewah/EWAHUtils.java

@@ -19,7 +19,7 @@ public class EWAHUtils {
 	 * @param bits - set of bits
 	 * @return Bitmap representation of set of ints
 	 */
-	public static EWAHCompressedBitmap converIndexSetToBitmap(Set<Integer> bits) {
+	public static EWAHCompressedBitmap convertIndexSetToBitmap(Set<Integer> bits) {
 		EWAHCompressedBitmap bm = new EWAHCompressedBitmap();
 		ArrayList<Integer> bitlist = new ArrayList<Integer>(bits);
 		Collections.sort(bitlist); // EWAH assumes sorted, otherwise silent failure

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/eval/data/SimulatedDataTest.java

@@ -257,7 +257,7 @@ public void testLiftOneAnnotations() throws Exception {
 			}
 			//for each individual, the things removed == original
 			LOG.info("i= "+i+" orig="+origBM.toString()+" removed="+removedCBits.toString()+" in "+derivedBMs.length+" sets");
-			Assert.assertTrue("Bits missing: "+origBM.andNot(EWAHUtils.converIndexSetToBitmap(removedCBits)), origBM.andNotCardinality(EWAHUtils.converIndexSetToBitmap(removedCBits))==0);
+			Assert.assertTrue("Bits missing: "+origBM.andNot(EWAHUtils.convertIndexSetToBitmap(removedCBits)), origBM.andNotCardinality(EWAHUtils.convertIndexSetToBitmap(removedCBits))==0);
 		}
 	}