Fix RSPEC-1940 boolean checks

JasonKamsu · JasonKamsu · commit 0af196ffd522 · 2025-11-21T08:24:39.000+01:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -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);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -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);
 	}
 
 	/**
@@ -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();
 	}
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -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 '.'" );
 		}
@@ -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 '.'" );
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -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
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -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;
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -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;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -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;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -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) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -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);
 				}

Original file line number	Diff line number	Diff line change
`@@ -260,7 +260,9 @@ private List<Location> parseLocationString(String string, int versus) {`
`260`	`260`	`l.setPartialOn3prime(true);`
`261`	`261`	`}`
`262`	`262`
`263`		`- if (!(accession == null \|\| "".equals(accession))) l.setAccession(new AccessionID(accession));`
	`263`	`+ if (accession != null && !"".equals(accession)) {`
	`264`	`+ l.setAccession(new AccessionID(accession));`
	`265`	`+ }`
`264`	`266`
`265`	`267`	`boundedLocationsCollection.add(l);`
`266`	`268`
Original file line number	Diff line number	Diff line change
`@@ -135,7 +135,7 @@ public static Location fromBio( int start, int end, char strand )`
`135`	`135`	`int s= start - 1;`
`136`	`136`	`int e= end;`
`137`	`137`
`138`		`- if( !( strand == '-' \|\| strand == '+' \|\| strand == '.' ))`
	`138`	`+ if( strand != '-' && strand != '+' && strand != '.' )`
`139`	`139`	`{`
`140`	`140`	`throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );`
`141`	`141`	`}`
`@@ -166,7 +166,7 @@ public static Location fromBioExt( int start, int length, char strand, int total`
`166`	`166`	`int s= start;`
`167`	`167`	`int e= s + length;`
`168`	`168`
`169`		`- if( !( strand == '-' \|\| strand == '+' \|\| strand == '.' ))`
	`169`	`+ if( strand != '-' && strand != '+' && strand != '.' )`
`170`	`170`	`{`
`171`	`171`	`throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );`
`172`	`172`	`}`
Original file line number	Diff line number	Diff line change
`@@ -62,7 +62,7 @@ public boolean equals(Object obj) {`
`62`	`62`	`if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {`
`63`	`63`	`return false;`
`64`	`64`	`}`
`65`		`- return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));`
	`65`	`+ return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);`
`66`	`66`	`}`
`67`	`67`
`68`	`68`	`@Override`
Original file line number	Diff line number	Diff line change
`@@ -424,7 +424,7 @@ public boolean isHeavyAtom() {`
`424`	`424`	`* @return <CODE>true</CODE> if Element is not Hydrogen and not Carbon.`
`425`	`425`	`*/`
`426`	`426`	`public boolean isHeteroAtom() {`
`427`		`- return !(this == C \|\| this == H);`
	`427`	`+ return this != C && this != H;`
`428`	`428`	`}`
`429`	`429`
`430`	`430`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str`
`1450`	`1450`	`//afpChain.setTotalRmsdOpt(rmsd);`
`1451`	`1451`	`//System.out.println("rmsd: " + rmsd);`
`1452`	`1452`
`1453`		`- if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {`
	`1453`	`+ if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {`
`1454`	`1454`	`rmsdLen=rmsd;`
`1455`	`1455`	`isRmsdLenAssigned=true;`
`1456`	`1456`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str`
`1455`	`1455`	`//afpChain.setTotalRmsdOpt(rmsd);`
`1456`	`1456`	`//System.out.println("rmsd: " + rmsd);`
`1457`	`1457`
`1458`		`- if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {`
	`1458`	`+ if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {`
`1459`	`1459`	`rmsdLen=rmsd;`
`1460`	`1460`	`isRmsdLenAssigned=true;`
`1461`	`1461`	`}`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {`
`55`	`55`	`if (first < 0 \|\| last < 0) {`
`56`	`56`	`return true;`
`57`	`57`	`}`
`58`		`- return ! (first == 0 && last > first);`
	`58`	`+ return first != 0 \|\| last <= first;`
`59`	`59`	`}`
`60`	`60`
`61`	`61`	`public static List<String> parseUnaryOperatorExpression(String operatorExpression) {`
Original file line number	Diff line number	Diff line change
`@@ -57,7 +57,7 @@ public static List<SecStrucInfo> getSecStrucInfo(Structure s) {`
`57`	`57`	`Group g = iter.next();`
`58`	`58`	`if (g.hasAminoAtoms()) {`
`59`	`59`	`Object p = g.getProperty(Group.SEC_STRUC);`
`60`		`- if (!(p == null)) {`
	`60`	`+ if (p != null) {`
`61`	`61`	`SecStrucInfo ss = (SecStrucInfo) p;`
`62`	`62`	`listSSI.add(ss);`
`63`	`63`	`}`