Merge pull request #1119 from Pasjonat90D/fix/use-isempty-instead-of-size-#1079

josemduarte · web-flow · commit 70e9a742425a · 2025-12-08T15:56:52.000-08:00
Fix #1079: Use isEmpty() instead of size() == 0
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -411,7 +411,7 @@ private void setLocation(List<Step> steps) {
 		}
 
 		// combine sublocations into 1 Location
-		if (sublocations.size() == 0) {
+		if (sublocations.isEmpty()) {
 			location = null;
 		} else if (sublocations.size() == 1) {
 			location = sublocations.get(0);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -119,7 +119,7 @@ public void addIntronsUsingExons() throws Exception {
 		if (intronAdded) { //going to assume introns are correct
 			return;
 		}
-		if (exonSequenceList.size() == 0) {
+		if (exonSequenceList.isEmpty()) {
 			return;
 		}
 		ExonComparator exonComparator = new ExonComparator();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
@@ -44,7 +44,7 @@ public class SequenceAsStringHelper<C extends Compound> {
 	 */
 	public String getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand) {
 		// TODO Optimise/cache.
-		if(parsedCompounds.size() == 0)
+		if(parsedCompounds.isEmpty())
 			return "";
 		StringBuilder builder = new StringBuilder();
 		if (strand.equals(Strand.NEGATIVE)) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
@@ -72,7 +72,7 @@ public void declareNamespace(String nsURI, String prefixHint)
 	private void handleDeclaredNamespaces()
 		throws IOException
 	{
-		if (namespacesDeclared.size() == 0) {
+		if (namespacesDeclared.isEmpty()) {
 			for (Iterator<String> nsi = namespacesDeclared.iterator(); nsi.hasNext(); ) {
 				String nsURI = nsi.next();
 				if (!namespacePrefixes.containsKey(nsURI)) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
@@ -126,7 +126,7 @@ private void setPrefSize() {
 	public void setAligMap(List<AlignedPosition> apos){
 		this.apos = apos;
 
-		if ( apos.size() == 0)
+		if (apos.isEmpty())
 			return;
 
 		AlignedPosition last = apos.get(apos.size()-1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
@@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
 
 			}
 			clusters.add(currentCluster);
-			if ( remainList.size() == 0) {
+			if ( remainList.isEmpty()) {
 				break;
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -127,7 +127,7 @@ public void setAlignRes(List<List<Integer>> alignRes) {
 	public int length() {
 		if (alignRes == null)
 			return 0;
-		if (alignRes.size() == 0)
+		if (alignRes.isEmpty())
 			return 0;
 		return alignRes.get(0).size();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -179,7 +179,7 @@ public int size() {
 		// Get the size from the variables that can contain the information
 		if (parent != null)
 			return parent.size();
-		else if (getBlocks().size() == 0) {
+		else if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		} else
@@ -194,7 +194,7 @@ public int getCoreLength() {
 	}
 
 	protected void updateLength() {
-		if (getBlocks().size() == 0) {
+		if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		}
@@ -207,7 +207,7 @@ protected void updateLength() {
 	}
 
 	protected void updateCoreLength() {
-		if (getBlocks().size() == 0) {
+		if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -207,7 +207,7 @@ public int getCoreLength() {
 	 * lengths.
 	 */
 	protected void updateLength() {
-		if (getBlockSets().size() == 0) {
+		if (getBlockSets().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty MultipleAlignment: blockSets size == 0.");
 		} // Otherwise try to calculate it from the BlockSet information
@@ -223,7 +223,7 @@ protected void updateLength() {
 	 * BlockSet core lengths.
 	 */
 	protected void updateCoreLength() {
-		if (getBlockSets().size() == 0) {
+		if (getBlockSets().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty MultipleAlignment: blockSets size == 0.");
 		} // Otherwise try to calculate it from the BlockSet information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
 		for (Block b : toDelete) {
 			for (BlockSet bs : msa.getBlockSets()) {
 				bs.getBlocks().remove(b);
-				if (bs.getBlocks().size() == 0)
+				if (bs.getBlocks().isEmpty())
 					emptyBs.add(bs);
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -117,7 +117,7 @@ public void setSubunitMap(Map<Integer, Integer> subunitMap) {
 					"Subunit Map index higher than Subunit List size.");
 
 		// Update the relation enum
-		if (subunitMap.size() == 0) {
+		if (subunitMap.isEmpty()) {
 			relation = QsRelation.DIFFERENT;
 		} else if (subunitMap.keySet().size() == subunits1.size()) {
 			if (subunitMap.values().size() == subunits2.size()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -228,7 +228,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 			throws StructureException, IOException {
 		return getBiologicalAssembly(new PdbId(pdbId), bioAssemblyId, multiModel);
 	}
-	
+
 	/**
 	 * Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
 	 * assembly from the biounit annotations found in {@link Structure#getPDBHeader()}
@@ -284,7 +284,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
 				asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
 
-		if (transformations == null || transformations.size() == 0) {
+		if (transformations == null || transformations.isEmpty()) {
 			throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
 		}
 
@@ -339,7 +339,7 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
 				asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
 
-		if (transformations == null || transformations.size() == 0) {
+		if (transformations == null || transformations.isEmpty()) {
 			throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
 		}
 
@@ -385,7 +385,7 @@ public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel)
 			List<BiologicalAssemblyTransformation> transformations =
 					asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
-			if (transformations == null || transformations.size() == 0) {
+			if (transformations == null || transformations.isEmpty()) {
 				logger.info("Could not load transformations to recreate biological assembly id {} of {}. Assembly " +
 						"id will be missing in biological assemblies.", bioAssemblyId, pdbId);
 				continue;
@@ -807,7 +807,7 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
 	public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 		if (pdbId == null)
 			return null;
-		
+
 		while (checkLoading(pdbId)) {
 			// waiting for loading to be finished...
 			try {
@@ -833,7 +833,7 @@ public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
 		return loadStructureFromCifByPdbId(new PdbId(pdbId));
 	}
-	
+
 	protected Structure loadStructureFromCifByPdbId(PdbId pdbId) throws IOException {
 		logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
 		Structure s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
@@ -120,7 +120,7 @@ public ChemComp getChemComp(String recordName) {
         }
 
         // If a null record or an empty chemcomp, return a default ChemComp and blacklist.
-        if (cc == null || (null == cc.getName() && cc.getAtoms().size() == 0)) {
+        if (cc == null || (null == cc.getName() && cc.getAtoms().isEmpty())) {
             s_logger.info("Unable to find or download {} - excluding from future searches.", recordName);
             unavailable.add(recordName);
             return getEmptyChemComp(recordName);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -331,7 +331,7 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
 			}
 		}
 
-		if (thisAligned.size() == 0 && otherAligned.size() == 0) {
+		if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
 			logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -58,7 +58,7 @@ public static Stoichiometry cluster(Structure structure,
 
 	public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererParameters params) {
 		List<SubunitCluster> clusters = new ArrayList<>();
-		if (subunits.size() == 0)
+		if (subunits.isEmpty())
 			return new Stoichiometry(clusters);
 
 		// First generate a new cluster for each Subunit
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -72,7 +72,7 @@ public void addPoint(Point3d point, double mass) {
 
 	public Point3d getCenterOfMass() {
 
-		if (points.size() == 0) {
+		if (points.isEmpty()) {
 			throw new IllegalStateException(
 					"MomentsOfInertia: no points defined");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1970,7 +1970,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 		// build it up.
 
 		if ( groupCode3.equals(currentGroup.getPDBName())) {
-			if ( currentGroup.getAtoms().size() == 0) {
+			if ( currentGroup.getAtoms().isEmpty()) {
 				//System.out.println("current group is empty " + current_group + " " + altLoc);
 				return currentGroup;
 			}
@@ -2762,7 +2762,7 @@ private void makeCompounds(List<String> compoundList,
 		}
 		//		System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
 		// since we're starting again from the first compound, reset it here
-		if ( entities.size() == 0){
+		if ( entities.isEmpty()){
 			current_compound = new EntityInfo();
 		} else {
 			current_compound = entities.get(0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -396,7 +396,7 @@ private Group getCorrectAltLocGroup(Character altLoc) {
 		}
 		// no matching altLoc group found.
 		// build it up.
-		if (group.getAtoms().size() == 0) {
+		if (group.getAtoms().isEmpty()) {
 			return group;
 		}
 		Group altLocG = (Group) group.clone();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -279,7 +279,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,
 			return centroid;
 		}
 
-		if ( transformations.size() == 0) {
+		if ( transformations.isEmpty()) {
 			return Calc.getCentroid(atoms).getCoords();
 
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -205,7 +205,7 @@ private void addChainMultiModel(Structure s, Chain newChain, String transformId)
 
 		// multi-model bioassembly
 
-		if ( modelIndex.size() == 0)
+		if (modelIndex.isEmpty())
 			modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
 
 		int modelCount = modelIndex.indexOf(transformId);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -64,7 +64,7 @@ public Map<Integer[], Integer> getInteractingRepeatUnits() {
 
 private void run() {
 	this.repeatUnitCenters = calcRepeatUnitCenters();
-	if (this.repeatUnitCenters.size() == 0) {
+	if (this.repeatUnitCenters.isEmpty()) {
 		return;
 	}
 	this.repeatUnits = calcRepeatUnits();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -98,7 +98,7 @@ public void complete() {
 
 	public String getPointGroup() {
 		if (modified) {
-			if (rotations.size() == 0) {
+			if (rotations.isEmpty()) {
 				return "C1";
 			}
 			complete();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -305,7 +305,7 @@ private boolean isSpherical() {
 	 * @return null if invalid, or a rotation if valid
 	 */
 	private Rotation isValidPermutation(List<Integer> permutation) {
-		if (permutation.size() == 0) {
+		if (permutation.isEmpty()) {
 			return null;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -145,7 +145,7 @@ private void completeRotationGroup() {
 	}
 
 	private boolean isValidPermutation(List<Integer> permutation) {
-		if (permutation.size() == 0) {
+		if (permutation.isEmpty()) {
 			return false;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
@@ -166,7 +166,7 @@ private List<T> getBoxTwo(long location) {
 		}
 		// ensure that boxTwo has no empty element by copying from tempBox of defined size
 		List<T> boxTwo = null;
-		if (tempBox.size() == 0) {
+		if (tempBox.isEmpty()) {
 			boxTwo = Collections.emptyList();
 		} else if (tempBox.size() == 1) {
 			boxTwo = Collections.singletonList(tempBox.get(0));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -645,10 +645,10 @@ public List<String> getTransfAlgebraic() {
 
 	public void setTransfAlgebraic(List<String> transfAlgebraic) {
 		//System.out.println("setting transfAlgebraic " + transfAlgebraic);
-		if ( transformations == null || transformations.size() == 0)
+		if ( transformations == null || transformations.isEmpty())
 			transformations = new ArrayList<Matrix4d>(transfAlgebraic.size());
 
-		if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0)
+		if ( this.transfAlgebraic == null || this.transfAlgebraic.isEmpty())
 			this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size());
 
 		for ( String transf : transfAlgebraic){
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -76,7 +76,7 @@ private void paintTable(Graphics g) {
 			sfiHashMap = sfi.getStrataInfoHashMap();
 		}
 
-		if(sfiHashMap.size() == 0)
+		if(sfiHashMap.isEmpty())
 			return;
 		//int height = this.getHeight();
 
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -140,7 +140,7 @@ public int compareTo(HmmerResult o) {
 		return(me.getSqFrom().compareTo(other.getSqFrom()));
 	}
 	private boolean emptyDomains(HmmerResult o) {
-		if ( o.getDomains() == null || o.getDomains().size() == 0)
+		if ( o.getDomains() == null || o.getDomains().isEmpty())
 			return true;
 		return false;
 	}

Original file line number	Diff line number	Diff line change
`@@ -411,7 +411,7 @@ private void setLocation(List<Step> steps) {`
`411`	`411`	`}`
`412`	`412`
`413`	`413`	`// combine sublocations into 1 Location`
`414`		`- if (sublocations.size() == 0) {`
	`414`	`+ if (sublocations.isEmpty()) {`
`415`	`415`	`location = null;`
`416`	`416`	`} else if (sublocations.size() == 1) {`
`417`	`417`	`location = sublocations.get(0);`
Original file line number	Diff line number	Diff line change
`@@ -119,7 +119,7 @@ public void addIntronsUsingExons() throws Exception {`
`119`	`119`	`if (intronAdded) { //going to assume introns are correct`
`120`	`120`	`return;`
`121`	`121`	`}`
`122`		`- if (exonSequenceList.size() == 0) {`
	`122`	`+ if (exonSequenceList.isEmpty()) {`
`123`	`123`	`return;`
`124`	`124`	`}`
`125`	`125`	`ExonComparator exonComparator = new ExonComparator();`
Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,7 @@ public void declareNamespace(String nsURI, String prefixHint)`
`72`	`72`	`private void handleDeclaredNamespaces()`
`73`	`73`	`throws IOException`
`74`	`74`	`{`
`75`		`- if (namespacesDeclared.size() == 0) {`
	`75`	`+ if (namespacesDeclared.isEmpty()) {`
`76`	`76`	`for (Iterator<String> nsi = namespacesDeclared.iterator(); nsi.hasNext(); ) {`
`77`	`77`	`String nsURI = nsi.next();`
`78`	`78`	`if (!namespacePrefixes.containsKey(nsURI)) {`
Original file line number	Diff line number	Diff line change
`@@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){`
`102`	`102`
`103`	`103`	`}`
`104`	`104`	`clusters.add(currentCluster);`
`105`		`- if ( remainList.size() == 0) {`
	`105`	`+ if ( remainList.isEmpty()) {`
`106`	`106`	`break;`
`107`	`107`	`}`
`108`	`108`	`}`
Original file line number	Diff line number	Diff line change
`@@ -127,7 +127,7 @@ public void setAlignRes(List<List<Integer>> alignRes) {`
`127`	`127`	`public int length() {`
`128`	`128`	`if (alignRes == null)`
`129`	`129`	`return 0;`
`130`		`- if (alignRes.size() == 0)`
	`130`	`+ if (alignRes.isEmpty())`
`131`	`131`	`return 0;`
`132`	`132`	`return alignRes.get(0).size();`
`133`	`133`	`}`
Original file line number	Diff line number	Diff line change
`@@ -179,7 +179,7 @@ public int size() {`
`179`	`179`	`// Get the size from the variables that can contain the information`
`180`	`180`	`if (parent != null)`
`181`	`181`	`return parent.size();`
`182`		`- else if (getBlocks().size() == 0) {`
	`182`	`+ else if (getBlocks().isEmpty()) {`
`183`	`183`	`throw new IndexOutOfBoundsException(`
`184`	`184`	`"Empty BlockSet: number of Blocks == 0.");`
`185`	`185`	`} else`
`@@ -194,7 +194,7 @@ public int getCoreLength() {`
`194`	`194`	`}`
`195`	`195`
`196`	`196`	`protected void updateLength() {`
`197`		`- if (getBlocks().size() == 0) {`
	`197`	`+ if (getBlocks().isEmpty()) {`
`198`	`198`	`throw new IndexOutOfBoundsException(`
`199`	`199`	`"Empty BlockSet: number of Blocks == 0.");`
`200`	`200`	`}`
`@@ -207,7 +207,7 @@ protected void updateLength() {`
`207`	`207`	`}`
`208`	`208`
`209`	`209`	`protected void updateCoreLength() {`
`210`		`- if (getBlocks().size() == 0) {`
	`210`	`+ if (getBlocks().isEmpty()) {`
`211`	`211`	`throw new IndexOutOfBoundsException(`
`212`	`212`	`"Empty BlockSet: number of Blocks == 0.");`
`213`	`213`	`}`
Original file line number	Diff line number	Diff line change
`@@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,`
`153`	`153`	`for (Block b : toDelete) {`
`154`	`154`	`for (BlockSet bs : msa.getBlockSets()) {`
`155`	`155`	`bs.getBlocks().remove(b);`
`156`		`- if (bs.getBlocks().size() == 0)`
	`156`	`+ if (bs.getBlocks().isEmpty())`
`157`	`157`	`emptyBs.add(bs);`
`158`	`158`	`}`
`159`	`159`	`}`