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Fix RSPEC-1940 boolean checks #1118

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Merged
josemduarte merged 1 commit into from
Dec 4, 2025
Merged

Fix RSPEC-1940 boolean checks #1118

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4 changes: 3 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,9 @@ private List<Location> parseLocationString(String string, int versus) {
l.setPartialOn3prime(true);
}

if (!(accession == null || "".equals(accession))) l.setAccession(new AccessionID(accession));
if (accession != null && !"".equals(accession)) {
l.setAccession(new AccessionID(accession));
}

boundedLocationsCollection.add(l);

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16 changes: 14 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
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Expand Up @@ -49,7 +49,13 @@ public static boolean equal(boolean one, boolean two) {
* @see #classEqual(Object, Object)
*/
public static boolean equal(Object one, Object two) {
return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
if (one == two) {
return true;
}
if (one == null || two == null) {
return false;
}
return one.equals(two);
}

/**
Expand Down Expand Up @@ -84,6 +90,12 @@ public static boolean equal(Object one, Object two) {
* equal at the class level
*/
public static boolean classEqual(Object one, Object two) {
return one == two || !(one == null || two == null) && one.getClass() == two.getClass();
if (one == two) {
return true;
}
if (one == null || two == null) {
return false;
}
return one.getClass() == two.getClass();
}
}
4 changes: 2 additions & 2 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
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Expand Up @@ -135,7 +135,7 @@ public static Location fromBio( int start, int end, char strand )
int s= start - 1;
int e= end;

if( !( strand == '-' || strand == '+' || strand == '.' ))
if( strand != '-' && strand != '+' && strand != '.' )
{
throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
}
Expand Down Expand Up @@ -166,7 +166,7 @@ public static Location fromBioExt( int start, int length, char strand, int total
int s= start;
int e= s + length;

if( !( strand == '-' || strand == '+' || strand == '.' ))
if( strand != '-' && strand != '+' && strand != '.' )
{
throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
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Expand Up @@ -62,7 +62,7 @@ public boolean equals(Object obj) {
if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
return false;
}
return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);
}

@Override
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
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Expand Up @@ -424,7 +424,7 @@ public boolean isHeavyAtom() {
* @return <CODE>true</CODE> if Element is not Hydrogen and not Carbon.
*/
public boolean isHeteroAtom() {
return !(this == C || this == H);
return this != C && this != H;
}

/**
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
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Expand Up @@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);

if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
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2 changes: 1 addition & 1 deletion ...ava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
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Expand Up @@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);

if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
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Expand Up @@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {
if (first < 0 || last < 0) {
return true;
}
return ! (first == 0 && last > first);
return first != 0 || last <= first;
}

public static List<String> parseUnaryOperatorExpression(String operatorExpression) {
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
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Expand Up @@ -57,7 +57,7 @@ public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
Group g = iter.next();
if (g.hasAminoAtoms()) {
Object p = g.getProperty(Group.SEC_STRUC);
if (!(p == null)) {
if (p != null) {
SecStrucInfo ss = (SecStrucInfo) p;
listSSI.add(ss);
}
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