biojava · Pasjonat90D · Dec 14, 2025
diff --git a/...e/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/...e/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -162,7 +162,7 @@ so it should be done here (manualy).
 		logger.info("taxonomy name '{}'", taxonName);
 		Assert.assertNotNull(taxonName);
 
-		if (seq.getFeaturesByType("CDS").size() > 0) {
+		if (!seq.getFeaturesByType("CDS").isEmpty()) {
 			FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
 			logger.info("CDS: {}", CDS);
 			String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -36,7 +36,7 @@
 
 /**
  *
- * @author Scooter Willis 
+ * @author Scooter Willis
  */
 public class GeneFeatureHelper {
 
@@ -418,7 +418,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
 			String startCodonName = "";
 			String stopCodonName = "";
 			FeatureList startCodonList = mRNAChildren.selectByType("five_prime_UTR");
-			if (startCodonList != null && startCodonList.size() > 0) {
+			if (startCodonList != null && !startCodonList.isEmpty()) {
 				startCodon = startCodonList.get(0);
 				if (strand == Strand.NEGATIVE) {
 					startCodonBegin = startCodon.location().bioEnd();
@@ -430,7 +430,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
 
 			FeatureList stopCodonList = mRNAChildren.selectByType("three_prime_UTR");
 
-			if (stopCodonList != null && stopCodonList.size() > 0) {
+			if (stopCodonList != null && !stopCodonList.isEmpty()) {
 				stopCodon = stopCodonList.get(0);
 				if (strand == Strand.NEGATIVE) {
 					stopCodonEnd = stopCodon.location().bioStart();
@@ -577,7 +577,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
 			String startCodonName = "";
 			String stopCodonName = "";
 			FeatureList startCodonList = gene.selectByAttribute("Note", "initial-exon");
-			if (startCodonList != null && startCodonList.size() > 0) {
+			if (startCodonList != null && !startCodonList.isEmpty()) {
 				startCodon = startCodonList.get(0);
 				if (strand == Strand.NEGATIVE) {
 					startCodonBegin = startCodon.location().bioEnd();
@@ -589,7 +589,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
 
 			FeatureList stopCodonList = gene.selectByAttribute("Note", "final-exon");
 
-			if (stopCodonList != null && stopCodonList.size() > 0) {
+			if (stopCodonList != null && !stopCodonList.isEmpty()) {
 				stopCodon = stopCodonList.get(0);
 				if (strand == Strand.NEGATIVE) {
 					stopCodonEnd = stopCodon.location().bioStart();
@@ -723,7 +723,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
 				String startCodonName = "";
 				String stopCodonName = "";
 				FeatureList startCodonList = transcriptFeature.selectByType("start_codon");
-				if (startCodonList != null && startCodonList.size() > 0) {
+				if (startCodonList != null && !startCodonList.isEmpty()) {
 					startCodon = startCodonList.get(0);
 					if (strand == Strand.POSITIVE) {
 						startCodonBegin = startCodon.location().bioStart();
@@ -735,7 +735,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
 
 				FeatureList stopCodonList = transcriptFeature.selectByType("stop_codon");
 
-				if (stopCodonList != null && stopCodonList.size() > 0) {
+				if (stopCodonList != null && !stopCodonList.isEmpty()) {
 					stopCodon = stopCodonList.get(0);
 					if (strand == Strand.POSITIVE) {
 						stopCodonEnd = stopCodon.location().bioEnd();

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -46,7 +46,7 @@
 
 /**
  *
- * @author Scooter Willis 
+ * @author Scooter Willis
  * @author Mark Chapman
  */
 public class GFF3FromUniprotBlastHits {
@@ -163,7 +163,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 								String notes = "";
 								if (featureKeyWords != null) {
 									List<String> keyWords = featureKeyWords.getKeyWords();
-									if (keyWords.size() > 0) {
+									if (!keyWords.isEmpty()) {
 										notes = ";Note=";
 										for (String note : keyWords) {
 											if ("Complete proteome".equals(note)) {
@@ -187,7 +187,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 									List<DBReferenceInfo> cazyList = databaseReferenceHashMap.get("CAZy");
 									List<DBReferenceInfo> goList = databaseReferenceHashMap.get("GO");
 									List<DBReferenceInfo> eccList = databaseReferenceHashMap.get("BRENDA");
-									if (pfamList != null && pfamList.size() > 0) {
+									if (pfamList != null && !pfamList.isEmpty()) {
 										if (notes.length() == 0) {
 											notes = ";Note=";
 										}
@@ -197,7 +197,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 										}
 									}
 
-									if (cazyList != null && cazyList.size() > 0) {
+									if (cazyList != null && !cazyList.isEmpty()) {
 										if (notes.length() == 0) {
 											notes = ";Note=";
 										}
@@ -208,7 +208,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 										}
 									}
 
-									if (eccList != null && eccList.size() > 0) {
+									if (eccList != null && !eccList.isEmpty()) {
 										if (notes.length() == 0) {
 											notes = ";Note=";
 										}
@@ -221,8 +221,8 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 										}
 									}
 
-									if (goList != null && goList.size() > 0) {
-										if (notes.length() == 0) {
+									if (goList != null && !goList.isEmpty()) {
+										if (notes.isEmpty()) {
 											notes = ";Note=";
 										}
 										for (DBReferenceInfo note : goList) {

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -31,7 +31,7 @@
 
 /**
  *
- * @author Scooter Willis 
+ * @author Scooter Willis
  */
 public class GFF3Writer {
 
@@ -122,7 +122,7 @@ public void write(OutputStream outputStream, Map<String, ChromosomeSequence> chr
 	private String getGFF3Note(List<String> notesList) {
 		String notes = "";
 
-		if (notesList.size() > 0) {
+		if (!notesList.isEmpty()) {
 			notes = ";Note=";
 			int noteindex = 1;
 			for (String note : notesList) {

diff --git a/...a-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java b/...a-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
@@ -53,7 +53,7 @@ public void test11GS() throws IOException, StructureException{
 
 		s = StructureIO.getStructure(pdbID);
 		assertNotNull(s);
-		assertTrue(s.getChains().size() > 0);
+		assertFalse(s.getChains().isEmpty());
 		Chain c = s.getChainByIndex(0);
 
 		assertTrue(c.getSeqResGroups().size() > 2);

diff --git a/...ava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/...ava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -69,7 +69,7 @@ public static String toXML(ModifiedCompound mc) throws IOException{
 
 
 		Set<StructureAtomLinkage > linkages = mc.getAtomLinkages();
-		if ( linkages.size() > 0 ) {
+		if (!linkages.isEmpty()) {
 			int pos = -1;
 			for ( StructureAtomLinkage link: linkages){
 				pos ++;

diff --git a/...inder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/...inder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
@@ -285,7 +285,7 @@ public void identify(final List<Chain> chains,
 
 		if (residues.isEmpty()) {
 			String pdbId = "?";
-			if ( chains.size() > 0) {
+			if (!chains.isEmpty()) {
 				Structure struc = chains.get(0).getStructure();
 				if ( struc != null)
 					pdbId = struc.getPDBCode();

diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
@@ -32,7 +32,8 @@
 import java.net.URL;
 import java.util.List;
 
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.fail;
 
 
@@ -100,11 +101,11 @@ public void testAcetylation() throws IOException {
 
 		List<Site> sites = Site.parseSites(localFile);
 
-		assertTrue(sites.size() > 0);
+		assertFalse(sites.isEmpty());
 
 		for (Site s : sites) {
 
-			assertTrue(s.getResidue() != null);
+			assertNotNull(s.getResidue());
 
 		}
 

diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
@@ -58,12 +58,12 @@ public WeakValueHashMap() {
 	private void diddleReferenceQueue() {
 	// Avoid making behind-the-scenes modifications while iterators exist.
 
-	if (iteratorRefs.size() > 0) {
+	if (!iteratorRefs.isEmpty()) {
 		Reference ref;
 		while ((ref = iteratorRefQueue.poll()) != null) {
 		iteratorRefs.remove(ref);
 		}
-		if (iteratorRefs.size() > 0) {
+		if (!iteratorRefs.isEmpty()) {
 		return;
 		}
 	}

diff --git a/...ture-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/...ture-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
@@ -229,7 +229,7 @@ public void keyReleased(KeyEvent e) {
 					list.ensureIndexIsVisible(list.getSelectedIndex() - 1);
 					return;
 				} else if (e.getKeyCode() == KeyEvent.VK_ENTER
-						&& list.getSelectedIndex() != -1 && suggestions.size() > 0) {
+						&& list.getSelectedIndex() != -1 && !suggestions.isEmpty()) {
 					setText((String) list.getSelectedValue());
 
 
@@ -365,7 +365,7 @@ public String doInBackground() {
 
 				setFont(regular);
 
-				if (suggestions.size() > 0) {
+				if (!suggestions.isEmpty()) {
 					list.setListData(suggestions);
 					list.setSelectedIndex(0);
 					list.ensureIndexIsVisible(0);

diff --git a/...c/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/...c/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
@@ -111,7 +111,7 @@ private List<ScopDomain> getPossibleScopDomains(String userInput) {
 			if ( stop.get())
 				return domains;
 
-			if ( domains == null || domains.size() < 1){
+			if ( domains == null || domains.isEmpty()){
 
 				if ( userInput.length() > 5){
 					// e.g. d4hhba
@@ -127,11 +127,11 @@ private List<ScopDomain> getPossibleScopDomains(String userInput) {
 			if (DEBUG)
 				System.out.println("domains: " + domains);
 
-			if ( domains == null || domains.size() < 1) {
+			if ( domains == null || domains.isEmpty()) {
 				if ( userInput.length() > 0 ){
 					List<ScopDescription> descs = scop.filterByClassificationId(userInput);
 
-					if ( descs == null || descs.size() < 1){
+					if ( descs == null || descs.isEmpty()){
 						descs = scop.filterByDescription(userInput);
 					}
 

diff --git a/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
@@ -74,7 +74,7 @@ public void actionPerformed(ActionEvent event) {
 		// check last command in history
 		// if equivalent, don't add,
 		// otherwise add
-		if (history.size()>0){
+		if (!history.isEmpty()){
 			String txt=history.get(history.size()-1);
 			if (! txt.equals(cmd)) {
 				history.add(cmd);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
@@ -83,7 +83,7 @@ public String toPDB() {
 
 	@Override
 	public void toPDB(StringBuffer buf) {
-		if (groups == null || groups.size() < 1) {
+		if (groups == null || groups.isEmpty()) {
 			return;
 		}
 

diff --git a/...src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/...src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -205,7 +205,7 @@ public static String toTransformMatrices(MultipleAlignment alignment) {
 
 			List<Matrix4d> btransforms = alignment.getBlockSet(bs)
 					.getTransformations();
-			if (btransforms == null || btransforms.size() < 1)
+			if (btransforms == null || btransforms.isEmpty())
 				continue;
 
 			if (alignment.getBlockSets().size() > 1) {

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1313,7 +1313,7 @@ public static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Ato
 		if ( afpChain.getBlockNum() > 0){
 
 			// Superimpose ligands relative to the first block
-			if( hetatms2.size() > 0 ) {
+			if(!hetatms2.isEmpty()) {
 
 				if ( afpChain.getBlockRotationMatrix().length > 0 ) {
 

diff --git a/...ucture/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/...ucture/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
@@ -169,7 +169,7 @@ else if ("ScoresCache".equals(child.getNodeName())){
 			}
 		}
 		//Because if it is 0 means that there were no transformations
-		if (transforms.size() != 0){
+		if (!transforms.isEmpty()){
 			bs.setTransformations(transforms);
 		}
 		return bs;

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
@@ -57,7 +57,7 @@ public void setPair(Pair<Group> pair) {
 	}
 
 	public double getMinDistance() {
-		if (atomContacts.size()==0) return 0;
+		if (atomContacts.isEmpty()) return 0;
 
 		double minDistance = Double.MAX_VALUE;
 		for (AtomContact atomContact:atomContacts) {

diff --git a/...va-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/...va-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -380,7 +380,7 @@ public List<StructureInterfaceCluster> getClusters(double contactOverlapScoreClu
 		clusters = new ArrayList<>();
 
 		// nothing to do if we have no interfaces
-		if (list.size()==0) return clusters;
+		if (list.isEmpty()) return clusters;
 
 		logger.debug("Calculating all-vs-all Jaccard scores for {} interfaces", list.size());
 		double[][] matrix = new double[list.size()][list.size()];

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -273,7 +273,7 @@ private void trimBondLists() {
 			for (Chain chain : structure.getChains(modelInd)) {
 				for (Group group : chain.getAtomGroups()) {
 					for (Atom atom : group.getAtoms()) {
-						if (atom.getBonds()!=null && atom.getBonds().size() > 0) {
+						if (atom.getBonds()!=null && !atom.getBonds().isEmpty()) {
 							((ArrayList<Bond>) atom.getBonds()).trimToSize();
 						}
 					}

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
@@ -1943,7 +1943,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 
 		// see if we know this altLoc already;
 		List<Atom> atoms = currentGroup.getAtoms();
-		if ( atoms.size() > 0) {
+		if (!atoms.isEmpty()) {
 			Atom a1 = atoms.get(0);
 			// we are just adding atoms to the current group
 			// probably there is a second group following later...
@@ -1956,7 +1956,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 		List<Group> altLocs = currentGroup.getAltLocs();
 		for ( Group altLocG : altLocs ){
 			atoms = altLocG.getAtoms();
-			if ( atoms.size() > 0) {
+			if (!atoms.isEmpty()) {
 				for ( Atom a1 : atoms) {
 					if (a1.getAltLoc().equals( altLoc)) {
 
@@ -2921,7 +2921,7 @@ private void triggerEndFileChecks(){
 			pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap());
 		}
 
-		if (ncsOperators !=null && ncsOperators.size()>0) {
+		if (ncsOperators !=null && !ncsOperators.isEmpty()) {
 			crystallographicInfo.setNcsOperators(
 				ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
 		}

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
@@ -198,7 +198,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
 			}
 		}
 
-		if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) {
+		if (atomRes.getAtomGroups(GroupType.AMINOACID).isEmpty()) {
 			logger.debug("ATOM chain {} does not contain amino acids, ignoring...", atomRes.getId());
 			return;
 		}
@@ -215,7 +215,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
 
 	private void alignNucleotideChains(Chain seqRes, Chain atomRes) {
 
-		if ( atomRes.getAtomGroups(GroupType.NUCLEOTIDE).size() < 1) {
+		if (atomRes.getAtomGroups(GroupType.NUCLEOTIDE).isEmpty()) {
 			logger.debug("ATOM chain {} does not contain nucleotides, ignoring...", atomRes.getId());
 
 			return;

diff --git a/...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/...a-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -372,7 +372,7 @@ public void consumeAtomSite(AtomSite atomSite) {
     private Group getAltLocGroup(String recordName, Character altLoc, Character oneLetterCode, String threeLetterCode,
                                  long seqId) {
         List<Atom> atoms = currentGroup.getAtoms();
-        if (atoms.size() > 0) {
+        if (!atoms.isEmpty()) {
             if (atoms.get(0).getAltLoc().equals(altLoc)) {
                 return currentGroup;
             }
@@ -381,7 +381,7 @@ private Group getAltLocGroup(String recordName, Character altLoc, Character oneL
         List<Group> altLocs = currentGroup.getAltLocs();
         for (Group altLocGroup : altLocs) {
             atoms = altLocGroup.getAtoms();
-            if (atoms.size() > 0) {
+            if (!atoms.isEmpty()) {
                 for (Atom a1 : atoms) {
                     if (a1.getAltLoc().equals(altLoc)) {
                         return altLocGroup;
@@ -1478,7 +1478,7 @@ private void setStructNcsOps() {
             }
         }
 
-        if (ncsOperators.size() > 0) {
+        if (!ncsOperators.isEmpty()) {
             structure.getCrystallographicInfo()
                     .setNcsOperators(ncsOperators.toArray(new Matrix4d[0]));
         }