Sonar S4973 "==" and "!=" should not be used when "equals" is overridden #1051
Description
My company develops software that performs automatic remediation of java code. This software detects defects identified for example by Sonar and automatically applies corrective measures. Maybe you would be interested that we experiment our product on your code? For example, we could submit PRs?
When we try the rule S4973 "==" and "!=" should not be used when "equals" is overridden
https://rules.sonarsource.com/java/RSPEC-1698
Below are the changes made by our software to correct this rule.
biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -140,7 +140,7 @@ public class GFF3FromUniprotBlastHits {
}
proteinIndex = proteinIndex + seq.length();
- if (startIndex != null && endIndex != null && startIndex != endIndex) {
+ if (startIndex != null && endIndex != null && !startIndex.equals(endIndex)) {
CDSSequence cdsSequence = cdsSequenceList.get(i);
String hitLabel = "";
if (transcriptSequence.getStrand() == Strand.POSITIVE) {
biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -140,7 +140,7 @@ public class GFF3FromUniprotBlastHits {
}
proteinIndex = proteinIndex + seq.length();
- if (startIndex != null && endIndex != null && startIndex != endIndex) {
+ if (startIndex != null && endIndex != null && !startIndex.equals(endIndex)) {
CDSSequence cdsSequence = cdsSequenceList.get(i);
String hitLabel = "";
if (transcriptSequence.getStrand() == Strand.POSITIVE) {
biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -373,7 +373,7 @@ public class EcodInstallation implements EcodDatabase {
return false;
// Re-download old copies of "latest"
- if(updateFrequency != null && requestedVersion == DEFAULT_VERSION ) {
+ if(updateFrequency != null && requestedVersion.equals(DEFAULT_VERSION) ) {
long mod = f.lastModified();
// Time of last update
Date lastUpdate = new Date();
biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -215,7 +215,7 @@ public class BondMaker {
for (Atom a2:a2s) {
if (a1.getAltLoc() != null && a2.getAltLoc()!=null &&
a1.getAltLoc()!=' ' && a2.getAltLoc()!=' ' &&
- a1.getAltLoc() != a2.getAltLoc()) {
+ !a1.getAltLoc().equals(a2.getAltLoc())) {
logger.debug("Skipping bond between atoms with differently named alt locs {} (altLoc '{}') -- {} (altLoc '{}')",
a1.toString(), a1.getAltLoc(), a2.toString(), a2.getAltLoc());
continue;
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -366,7 +366,7 @@ public class HelixSolver {
int permutation = -1;
double minDistSq = Double.MAX_VALUE;
for (int j = 0; j < centers.size(); j++) {
- if (seqClusterId.get(i) == seqClusterId.get(j)) {
+ if (seqClusterId.get(i) != null && seqClusterId.get(i).equals(seqClusterId.get(j))) {
if (!used[j]) {
double dSq = tCenter.distanceSquared(centers.get(j));
if (dSq < minDistSq && dSq <= rmsdThresholdSq) {
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -334,7 +334,7 @@ public class RotationSolver implements QuatSymmetrySolver {
int selfaligned = 0;
for (int i = 0; i < permutation.size(); i++) {
int j = permutation.get(i);
- if ( seqClusterId.get(i) != seqClusterId.get(j)) {
+ if ( seqClusterId.get(i) != null && !seqClusterId.get(i).equals(seqClusterId.get(j))) {
return false;
}
if(i == j ) {
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -176,7 +176,7 @@ public class SystematicSolver implements QuatSymmetrySolver {
List<Integer> seqClusterId = subunits.getClusterIds();
for (int i = 0; i < permutation.size(); i++) {
int j = permutation.get(i);
- if (seqClusterId.get(i) != seqClusterId.get(j)) {
+ if (seqClusterId.get(i) != null && !seqClusterId.get(i).equals(seqClusterId.get(j))) {
return false;
}
}