Merge pull request #1086 from jlerbsc/master

Fix sonar issue 2629 Logging arguments should not require evaluation
biojava · Mar 6, 2024 · 81e0544 · 81e0544
2 parents f94e577 + 1ac29b3
commit 81e0544
Show file tree

Hide file tree

Showing 24 changed files with 100 additions and 125 deletions.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -173,7 +173,7 @@ 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);

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/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;
  }

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/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);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/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;
  }

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/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;

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/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 ");
 

diff --git a/...ava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/...ava-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
 

diff --git a/...-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/...-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);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/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--) {

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
@@ -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;
  }
 

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java b/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);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/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);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/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()) &&

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/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());
  }
  }