biojava · josemduarte · Dec 8, 2025 · Nov 30, 2025
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/...ava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/...ava-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/...a-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/...a-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/...ucture/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/...ucture/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/...cture/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/...cture/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/...va-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/...va-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/...ucture/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/...ucture/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/...a-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/...a-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/...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/...va-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/...ava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/...ava-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/...rvival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/...rvival/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 change
@@ Expand Up @@
     			}
     			clusters.add(currentCluster);
-    			if ( remainList.size() == 0) {
+    			if ( remainList.isEmpty()) {
     				break;
     			}
     		}
@@ Expand Down @@