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SonarQube bugs #1060

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Merged
aalhossary merged 2 commits into from
May 9, 2023
Merged

SonarQube bugs #1060

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963dc01
Sonar S4973 '==' and '!=' should not be used when 'equals' is overrid…
tmrpavan Apr 16, 2023
caa5789
Sonar S4973 '==' and '!=' should not be used when 'equals' is overrid…
May 7, 2023
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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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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
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Expand Up @@ -214,8 +214,8 @@ private void formBondAltlocAware(Group g1, String name1, Group g2, String name2,
for (Atom a1:a1s) {
for (Atom a2:a2s) {
if (a1.getAltLoc() != null && a2.getAltLoc()!=null &&
a1.getAltLoc()!=' ' && a2.getAltLoc()!=' ' &&
a1.getAltLoc() != a2.getAltLoc()) {
!a1.getAltLoc().equals(' ') && !a2.getAltLoc().equals(' ') &&
!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 (Objects.equals(seqClusterId.get(i), seqClusterId.get(j))) {
if (!used[j]) {
double dSq = tCenter.distanceSquared(centers.get(j));
if (dSq < minDistSq && dSq <= rmsdThresholdSq) {
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27 changes: 15 additions & 12 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
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Expand Up @@ -21,12 +21,6 @@

package org.biojava.nbio.structure.symmetry.core;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import javax.vecmath.AxisAngle4d;
import javax.vecmath.Matrix4d;
Expand All @@ -40,6 +34,14 @@
import org.biojava.nbio.structure.symmetry.geometry.DistanceBox;
import org.biojava.nbio.structure.symmetry.geometry.SphereSampler;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;


/**
*
Expand Down Expand Up @@ -90,7 +92,7 @@ private void solve() {
// isSpherical check added 08-04-11
if (maxSymOps % 60 == 0 && isSpherical) {
maxSymOps = 60;
}
}

AxisAngle4d sphereAngle = new AxisAngle4d();
Matrix4d transformation = new Matrix4d();
Expand Down Expand Up @@ -122,7 +124,7 @@ private void solve() {

// get permutation of subunits and check validity/uniqueness
List<Integer> permutation = getPermutation();
// System.out.println("Rotation Solver: permutation: " + i + ": " + permutation);
// System.out.println("Rotation Solver: permutation: " + i + ": " + permutation);

// check if novel
if ( evaluatedPermutations.containsKey(permutation)) {
Expand Down Expand Up @@ -277,7 +279,7 @@ private List<Double> getAngles() {
int n = subunits.getSubunitCount();
// for spherical symmetric cases, n cannot be higher than 60
if (n % 60 == 0 && isSpherical()) {
n = 60;
n = 60;
}
List<Integer> folds = subunits.getFolds();
List<Double> angles = new ArrayList<Double>(folds.size()-1);
Expand Down Expand Up @@ -334,7 +336,7 @@ 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 (!Objects.equals(seqClusterId.get(i), seqClusterId.get(j))) {
return false;
}
if(i == j ) {
Expand All @@ -344,6 +346,7 @@ private boolean isAllowedPermutation(List<Integer> permutation) {
// either identity (all self aligned) or all unique
return selfaligned == 0 || selfaligned == permutation.size();
}

/**
* Adds translational component to rotation matrix
* @param rotation
Expand Down Expand Up @@ -407,7 +410,7 @@ private List<Integer> getPermutation() {
int closest = -1;
double minDist = Double.MAX_VALUE;

for (int j : neighbors) {
for (int j : neighbors) {
double dist = t.distanceSquared(originalCoords[j]);
if (dist < minDist) {
closest = j;
Expand All @@ -417,7 +420,7 @@ private List<Integer> getPermutation() {

sum += minDist;
if (closest == -1) {
break;
break;
}
permutation.add(closest);
}
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4 changes: 2 additions & 2 deletions ...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
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Expand Up @@ -30,10 +30,10 @@
import javax.vecmath.Point3d;
import javax.vecmath.Quat4d;
import javax.vecmath.Vector3d;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Set;


Expand Down 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 (!Objects.equals(seqClusterId.get(i), seqClusterId.get(j))) {
return false;
}
}
Expand Down