Fix sonar issue 2629 Logging arguments should not require evaluation

biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java

@@ -212,7 +212,7 @@ public static void createValidationFiles(URLConnection resourceUrlConnection, Fi
 		if(size == -1) {
 			logger.warn("could not find expected file size for resource {}.", resourceUrlConnection.getURL());
 		} else {
-			logger.debug("Content-Length: " + size);
+			logger.debug("Content-Length: {}", size);
 			File sizeFile = new File(localDestination.getParentFile(), localDestination.getName() + SIZE_EXT);
 			try (PrintStream sizePrintStream = new PrintStream(sizeFile)) {
 				sizePrintStream.print(size);

biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java

@@ -135,7 +135,7 @@ private void clusterIt() {
 		dendrogram = new LinkedPair[numItems-1];
 
 
-		logger.debug("Initial matrix: \n"+matrixToString());
+		logger.debug("Initial matrix: \n{}", matrixToString());
 
 
 		for (int m=0;m<numItems-1;m++) {
@@ -309,11 +309,11 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 					}
 				}
 
-				logger.debug("Within cutoff:     "+dendrogram[i]);
+				logger.debug("Within cutoff:     {}", dendrogram[i]);
 
 			} else {
 
-				logger.debug("Not within cutoff: "+dendrogram[i]);
+				logger.debug("Not within cutoff: {}", dendrogram[i]);
 
 			}
 		}
@@ -344,7 +344,7 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 
 		}
 
-		logger.debug("Clusters: \n"+clustersToString(finalClusters));
+		logger.debug("Clusters: \n{}", clustersToString(finalClusters));
 
 		return finalClusters;
 	}

biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java

@@ -231,12 +231,12 @@ public static int getCDSLength(GeneChromosomePosition chromPos) {
 	 */
 	public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos) {
 
-		logger.debug(" ? Checking chromosome position for CDS position " + cdsNucleotidePosition);
+		logger.debug(" ? Checking chromosome position for CDS position {}", cdsNucleotidePosition);
 
 		List<Integer> exonStarts = chromPos.getExonStarts();
 		List<Integer> exonEnds = chromPos.getExonEnds();
 
-		logger.debug(" Exons:" + exonStarts.size());
+		logger.debug(" Exons:{}", exonStarts.size());
 
 		int cdsStart = chromPos.getCdsStart();
 		int cdsEnd = chromPos.getCdsEnd();
@@ -378,7 +378,7 @@ public static ChromPos getChromPosReverse(int cdsPos, List<Integer> exonStarts,
 
 					if ( tmp > (end - start ) ) {
 						tmp = (end - start );
-						logger.debug("changing tmp to " + tmp);
+						logger.debug("changing tmp to {}", tmp);
 					}
 					logger.debug("     " + cdsPos + " " + codingLength + " | " + (cdsPos - codingLength) + " | " + (end -start) + " | " + tmp);
 					logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start) + " | " + codingLength + " | " + (codingLength % 3));
@@ -397,7 +397,7 @@ public static ChromPos getChromPosReverse(int cdsPos, List<Integer> exonStarts,
 			logger.debug("     coding length: " + codingLength + "(phase:" + (codingLength % 3) + ") CDS POS trying to map:" + cdsPos);
 		}
 
-		logger.debug("length exons: " + lengthExons);
+		logger.debug("length exons: {}", lengthExons);
 		// could not map, or map over the full length??
 		return new ChromPos(-1,-1);
 
@@ -811,11 +811,11 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
 
 		// the genetic coordinate is not in a coding region
 		if ( (chromPos < (cdsStart+base) ) || ( chromPos > (cdsEnd+base) ) ) {
-			logger.debug("The "+format(chromPos)+" position is not in a coding region");
+			logger.debug("The {} position is not in a coding region", format(chromPos));
 			return -1;
 		}
 
-		logger.debug("looking for CDS position for " +format(chromPos));
+		logger.debug("looking for CDS position for {}", format(chromPos));
 
 		// map the genetic coordinates of coding region on a stretch of a reverse strand
 		List<Range<Integer>> cdsRegions = getCDSRegions(exonStarts, exonEnds, cdsStart, cdsEnd);
@@ -858,11 +858,11 @@ public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<
 
 		// the genetic coordinate is not in a coding region
 		if ( (chromPos < (cdsStart+base)) || ( chromPos > (cdsEnd+base) ) ) {
-			logger.debug("The "+format(chromPos)+" position is not in a coding region");
+			logger.debug("The {} position is not in a coding region", format(chromPos));
 			return -1;
 		}
 
-		logger.debug("looking for CDS position for " +format(chromPos));
+		logger.debug("looking for CDS position for {}", format(chromPos));
 
 		// map the genetic coordinate on a stretch of a reverse strand
 		List<Range<Integer>> cdsRegions = getCDSRegions(exonStarts, exonEnds, cdsStart, cdsEnd);

biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java

@@ -597,14 +597,7 @@ public GroupType getPredominantGroupType(){
 				max = GroupType.HETATM;
 			}
 		}
-		logger.debug(
-				"Ratio of residues to total for chain with asym_id {} is below {}. Assuming it is a {} chain. "
-						+ "Counts: # aa residues: {}, # nuc residues: {}, # non-water het residues: {}, # waters: {}, "
-						+ "ratio aa/total: {}, ratio nuc/total: {}",
-				getId(), ratioResiduesToTotal, max, sizeAminos,
-				sizeNucleotides, sizeHetatomsWithoutWater, sizeWaters,
-				(double) sizeAminos / (double) fullSize,
-				(double) sizeNucleotides / (double) fullSize);
+		logger.debug("Ratio of residues to total for chain with asym_id {} is below {}. Assuming it is a {} chain. Counts: # aa residues: {}, # nuc residues: {}, # non-water het residues: {}, # waters: {}, ratio aa/total: {}, ratio nuc/total: {}{}{}{}{}", getId(), ratioResiduesToTotal, max, sizeAminos, sizeNucleotides, sizeHetatomsWithoutWater, sizeWaters, (double) sizeAminos, (double) fullSize, (double) sizeNucleotides, (double) fullSize);
 
 		return max;
 	}

biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java

@@ -834,10 +834,7 @@ public static Atom[] getAtomArray(Chain c, String[] atomNames) {
 			for (String atomName : atomNames) {
 				Atom a = g.getAtom(atomName);
 				if (a == null) {
-					logger.debug("Group " + g.getResidueNumber() + " ("
-							+ g.getPDBName()
-							+ ") does not have the required atom '" + atomName
-							+ "'");
+					logger.debug("Group {} ({}) does not have the required atom '{}'", g.getResidueNumber(), g.getPDBName(), atomName);
 					// this group does not have a required atom, skip it...
 					thisGroupAllAtoms = false;
 					break;

biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java

@@ -407,8 +407,8 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 
 		// step 1 get all Diagonals of length X that are similar between both
 		// structures
-		logger.debug(" length atoms1:" + ca1.length);
-		logger.debug(" length atoms2:" + ca2.length);
+		logger.debug(" length atoms1:{}", ca1.length);
+		logger.debug(" length atoms2:{}", ca2.length);
 
 		logger.debug("step 1 - get fragments with similar intramolecular distances ");
 

biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java

@@ -375,10 +375,10 @@ public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDi
 		List<JointFragments> fll = new ArrayList<JointFragments>();
 
 		double adiff = angleDiff * Math.PI / 180d;
-		logger.debug("addiff" + adiff);
+		logger.debug("addiff{}", adiff);
 		//distance between two unit vectors with angle adiff
 		double ddiff = Math.sqrt(2.0-2.0*Math.cos(adiff));
-		logger.debug("ddiff" + ddiff);
+		logger.debug("ddiff{}", ddiff);
 
 		// the fpairs in the flist have to be sorted with respect to their positions
 

biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java

@@ -140,7 +140,7 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object parameters)
 			throw new StructureException("Empty alignment for sequences "+s1+" and "+s2);
 		}
 
-		logger.debug("Smith-Waterman alignment is: "+pair.toString(100));
+		logger.debug("Smith-Waterman alignment is: {}", pair.toString(100));
 
 		// convert to a 3D alignment...
 		afpChain = convert(ca1,ca2,pair, smithWaterman);

biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java

@@ -82,7 +82,7 @@ public static List<Subunit> extractSubunits(Structure structure,
 		// Calculate the minimum length of a Subunit
 		int adjustedMinLen = calcAdjustedMinimumSequenceLength(subunits,
 				absMinLen, fraction, minLen);
-		logger.debug("Adjusted minimum sequence length: " + adjustedMinLen);
+		logger.debug("Adjusted minimum sequence length: {}", adjustedMinLen);
 
 		// Filter out short Subunits
 		for (int s = subunits.size() - 1; s >= 0; s--) {

biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java

@@ -468,13 +468,13 @@ public String toString() {
 	public static StructureInterfaceList calculateInterfaces(Structure struc) {
 		CrystalBuilder builder = new CrystalBuilder(struc);
 		StructureInterfaceList interfaces = builder.getUniqueInterfaces();
-		logger.debug("Calculating ASA for "+interfaces.size()+" potential interfaces");
+		logger.debug("Calculating ASA for {} potential interfaces", interfaces.size());
 		interfaces.calcAsas(StructureInterfaceList.DEFAULT_ASA_SPHERE_POINTS, //fewer for performance
 				Runtime.getRuntime().availableProcessors(),
 				StructureInterfaceList.DEFAULT_MIN_COFACTOR_SIZE);
 		interfaces.removeInterfacesBelowArea();
 		interfaces.getClusters();
-		logger.debug("Found "+interfaces.size()+" interfaces");
+		logger.debug("Found {} interfaces", interfaces.size());
 		return interfaces;
 	}
 

biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java

@@ -127,7 +127,7 @@ public Map<K,V> reloadFromFile() {
 
 		try{
 
-			logger.debug("Reloading from cache " + f.getAbsolutePath());
+			logger.debug("Reloading from cache {}", f.getAbsolutePath());
 
 			FileInputStream fis = new FileInputStream(f);
 			ObjectInputStream ois = new ObjectInputStream(fis);

biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java

@@ -261,13 +261,13 @@ private void calcRmsd(Point3d[] x, Point3d[] y) {
 			// translate to origin
 			xref = CalcPoint.clonePoint3dArray(x);
 			xtrans = CalcPoint.centroid(xref);
-			logger.debug("x centroid: " + xtrans);
+			logger.debug("x centroid: {}", xtrans);
 			xtrans.negate();
 			CalcPoint.translate(new Vector3d(xtrans), xref);
 
 			yref = CalcPoint.clonePoint3dArray(y);
 			ytrans = CalcPoint.centroid(yref);
-			logger.debug("y centroid: " + ytrans);
+			logger.debug("y centroid: {}", ytrans);
 			ytrans.negate();
 			CalcPoint.translate(new Vector3d(ytrans), yref);
 			innerProduct(yref, xref);

biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java

@@ -297,7 +297,7 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch
 
 					logger.debug("Alignment for chain pair {},{}: identity: {}, gap coverage 1: {}, gap coverage 2: {}",
 							c1.getId(), c2.getId(), String.format("%4.2f",identity), String.format("%4.2f",gapCov1), String.format("%4.2f",gapCov2));
-					logger.debug("\n"+pair.toString(100));
+					logger.debug("\n{}", pair.toString(100));
 
 					if (identity > IDENTITY_THRESHOLD && gapCov1<GAP_COVERAGE_THRESHOLD && gapCov2<GAP_COVERAGE_THRESHOLD) {
 						if (	!chainIds2entities.containsKey(c1.getId()) &&

biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java

@@ -436,7 +436,7 @@ public boolean deleteStructure(PdbId pdbId) throws IOException{
 				// delete file
 				boolean success = existing.delete();
 				if(success) {
-					logger.debug("Deleting "+existing.getAbsolutePath());
+					logger.debug("Deleting {}", existing.getAbsolutePath());
 				}
 				deleted = deleted || success;
 
@@ -445,7 +445,7 @@ public boolean deleteStructure(PdbId pdbId) throws IOException{
 				if(parent != null) {
 					success = parent.delete();
 					if(success) {
-						logger.debug("Deleting "+parent.getAbsolutePath());
+						logger.debug("Deleting {}", parent.getAbsolutePath());
 					}
 				}