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Sonar S4973 '==' and '!=' should not be used when 'equals' is overridden #1052

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Sonar S4973 '==' and '!=' should not be used when 'equals' is overridden #1052

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2 changes: 1 addition & 1 deletion biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
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Expand Up @@ -140,7 +140,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
}

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) {
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
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Expand Up @@ -373,7 +373,7 @@ private boolean domainsAvailable() {
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();
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
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Expand Up @@ -215,7 +215,7 @@ private void formBondAltlocAware(Group g1, String name1, Group g2, String name2,
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;
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
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Expand Up @@ -366,7 +366,7 @@ private List<Integer> getPermutation(Matrix4d transformation) {
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) {
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
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Expand Up @@ -334,7 +334,7 @@ private boolean isAllowedPermutation(List<Integer> permutation) {
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 ) {
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2 changes: 1 addition & 1 deletion ...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
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Expand Up @@ -176,7 +176,7 @@ private boolean isAllowedPermuation(List<Integer> permutation) {
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;
}
}
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