codacy issues fixed

src/main/java/org/jreliability/bdd/BDDConstraint.java

@@ -15,11 +15,13 @@
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
 import java.util.Set;
 
 /**
- * The {@link BDDConstraint} is used to model {@link greater-equal} constraints with a left-hand-side ({@link lhs})
- * consisting of {@link Literals} and the right-hand-side ({@link rhs}) being an {@link Integer}.
+ * The {@link BDDConstraint} is used to model {@link greater-equal} constraints
+ * with a left-hand-side ({@link lhs}) consisting of {@link Literals} and the
+ * right-hand-side ({@link rhs}) being an {@link Integer}.
  * 
  * @author glass, lukasiewycz
  * 
@@ -33,8 +35,8 @@ class BDDConstraint<T> {
 	 */
 	protected int rhs;
 	/**
-	 * The left-hand-side of the constraint as a {@link List} of {@link
-	 * Literals}.
+	 * The left-hand-side of the constraint as a {@link List} of
+	 * {@link Literals}.
 	 */
 	protected List<Literal<T>> lhs = new ArrayList<>();
 	/**
@@ -43,7 +45,8 @@ class BDDConstraint<T> {
 	protected Set<BDD<T>> variables = new HashSet<>();
 
 	/**
-	 * Constructs a {@link BDDConstraint} with a given right-hand-side {@link rhs} and left-hand-side {@link lhs}.
+	 * Constructs a {@link BDDConstraint} with a given right-hand-side
+	 * {@link rhs} and left-hand-side {@link lhs}.
 	 * 
 	 * @param rhs
 	 *            the right-hand-side
@@ -56,8 +59,9 @@ public BDDConstraint(int rhs, List<Literal<T>> lhs) {
 	}
 
 	/**
-	 * Initializes the {@link BDDConstraint} with the normalizing operations proposed by {@link Een & Soerrensson 2006}
-	 * plus zero coefficient elimination.
+	 * Initializes the {@link BDDConstraint} with the normalizing operations
+	 * proposed by {@link Een & Soerrensson 2006} plus zero coefficient
+	 * elimination.
 	 * 
 	 * @param literals
 	 *            the literals
@@ -73,8 +77,8 @@ protected void initialize(List<Literal<T>> literals) {
 	}
 
 	/**
-	 * Ensures a positive {@link coefficient} of the {@link Literal} by a negotiation of the variable and an update of
-	 * the {@link rhs}.
+	 * Ensures a positive {@link coefficient} of the {@link Literal} by a
+	 * negotiation of the variable and an update of the {@link rhs}.
 	 * 
 	 * @param literal
 	 *            the literal
@@ -92,8 +96,8 @@ protected void checkCoefficient(Literal<T> literal) {
 	}
 
 	/**
-	 * Checks the {@link Literal} if it includes a variable that is already present in the {@link BDDConstraint} and
-	 * adds it correctly.
+	 * Checks the {@link Literal} if it includes a variable that is already
+	 * present in the {@link BDDConstraint} and adds it correctly.
 	 * 
 	 * @param literal
 	 */
@@ -119,7 +123,8 @@ protected void checkAndAddVariable(Literal<T> literal) {
 	}
 
 	/**
-	 * Trims all {@link coefficients} that are greater than the {@link rhs} to {@link rhs}.
+	 * Trims all {@link coefficients} that are greater than the {@link rhs} to
+	 * {@link rhs}.
 	 */
 	protected void trim() {
 		for (Literal<T> literal : lhs) {
@@ -147,8 +152,9 @@ protected void eliminateZeroCoefficients() {
 	}
 
 	/**
-	 * Determines the greatest-common-divisor ({@link gcd}) of all {@link
-	 * coefficients} of the {@link lhs} and the {@link rhs} and updates the values.
+	 * Determines the greatest-common-divisor ({@link gcd}) of all
+	 * {@link coefficients} of the {@link lhs} and the {@link rhs} and updates
+	 * the values.
 	 */
 	protected void gcd() {
 		if (!lhs.isEmpty()) {
@@ -170,7 +176,8 @@ protected void gcd() {
 	}
 
 	/**
-	 * Returns the {@link gcd} of two {@link Integers} by a simple recursive procedure.
+	 * Returns the {@link gcd} of two {@link Integers} by a simple recursive
+	 * procedure.
 	 * 
 	 * @param a
 	 *            integer a
@@ -195,8 +202,8 @@ public int getRhs() {
 	}
 
 	/**
-	 * Returns the left-hand-side ({@link lhs}) of the constraint as a {@link
-	 * List} of {@link Literals}.
+	 * Returns the left-hand-side ({@link lhs}) of the constraint as a
+	 * {@link List} of {@link Literals}.
 	 * 
 	 * @return the lhs of the constraint
 	 */
@@ -205,7 +212,8 @@ public List<Literal<T>> getLhs() {
 	}
 
 	/**
-	 * The {@link Literal} represents a variable using a {@link BDD} and its {@link coefficient}.
+	 * The {@link Literal} represents a variable using a {@link BDD} and its
+	 * {@link coefficient}.
 	 * 
 	 * @author glass
 	 * 
@@ -217,15 +225,16 @@ static class Literal<T> {
 		/**
 		 * The coefficient.
 		 */
-		Integer coefficient = 0;
+		protected Integer coefficient = 0;
 
 		/**
 		 * The variable.
 		 */
-		BDD<T> variable = null;
+		protected BDD<T> variable = null;
 
 		/**
-		 * Constructs a {@link Literal} with a given coefficient and variable as a {@link BDD}.
+		 * Constructs a {@link Literal} with a given coefficient and variable as
+		 * a {@link BDD}.
 		 * 
 		 * @param coefficient
 		 *            the coefficient
@@ -287,7 +296,8 @@ public String toString() {
 	}
 
 	/**
-	 * The {@link Pair} represents a tuple of two {@link Objects} {@link A} and {@link B}.
+	 * The {@link Pair} represents a tuple of two {@link Objects} {@link A} and
+	 * {@link B}.
 	 * 
 	 * @author glass
 	 * 

src/main/java/org/jreliability/bdd/BDDTTRF.java

@@ -32,8 +32,9 @@
 import org.jreliability.function.ReliabilityFunction;
 
 /**
- * The {@link BDDTTRF} transforms a Boolean function represented as a {@link Term} into a {@link ReliabilityFunction}
- * or, if needed, into a {@link BDD}.
+ * The {@link BDDTTRF} transforms a Boolean function represented as a
+ * {@link Term} into a {@link ReliabilityFunction} or, if needed, into a
+ * {@link BDD}.
  * 
  * @author glass
  * 
@@ -60,8 +61,8 @@ public BDDTTRF(BDDProvider<T> provider) {
 	/*
 	 * (non-Javadoc)
 	 * 
-	 * @see org.jreliability.booleanfunction.TTRF#convert(org.jreliability. booleanfunction.Term,
-	 * org.apache.commons.collections15.Transformer)
+	 * @see org.jreliability.booleanfunction.TTRF#convert(org.jreliability.
+	 * booleanfunction.Term, org.apache.commons.collections15.Transformer)
 	 */
 	@Override
 	public ReliabilityFunction convert(Term term, Transformer<T, ReliabilityFunction> functionTransformer) {
@@ -71,8 +72,9 @@ public ReliabilityFunction convert(Term term, Transformer<T, ReliabilityFunction
 	/*
 	 * (non-Javadoc)
 	 * 
-	 * @see org.jreliability.booleanfunction.TTRF#convert(org.jreliability. booleanfunction.Term,
-	 * org.apache.commons.collections15.Transformer, org.apache.commons.collections15.Predicate)
+	 * @see org.jreliability.booleanfunction.TTRF#convert(org.jreliability.
+	 * booleanfunction.Term, org.apache.commons.collections15.Transformer,
+	 * org.apache.commons.collections15.Predicate)
 	 */
 	@Override
 	public ReliabilityFunction convert(Term term, Transformer<T, ReliabilityFunction> functionTransformer,
@@ -82,13 +84,15 @@ public ReliabilityFunction convert(Term term, Transformer<T, ReliabilityFunction
 	}
 
 	/**
-	 * Converts a given {@link BDD} and a {@link Transformer} to a {@link ReliabilityFunction}.
+	 * Converts a given {@link BDD} and a {@link Transformer} to a
+	 * {@link ReliabilityFunction}.
 	 * 
 	 * @param bdd
 	 *            the bdd
 	 * @param functionTransformer
 	 *            the function functionTransformer
-	 * @return a reliability function from the given bdd and function functionTransformer
+	 * @return a reliability function from the given bdd and function
+	 *         functionTransformer
 	 */
 	public ReliabilityFunction convert(BDD<T> bdd, Transformer<T, ReliabilityFunction> functionTransformer) {
 		BDDReliabilityFunction<T> function = new BDDReliabilityFunction<>(bdd, functionTransformer);
@@ -108,7 +112,8 @@ public BDD<T> convertToBDD(Term term) {
 	}
 
 	/**
-	 * Returns a {@link BDD} representing the given {@link Term} while respecting the exists-variables.
+	 * Returns a {@link BDD} representing the given {@link Term} while
+	 * respecting the exists-variables.
 	 * 
 	 * @param term
 	 *            the term
@@ -118,7 +123,7 @@ public BDD<T> convertToBDD(Term term) {
 	 */
 	public BDD<T> convertToBDD(Term term, Predicate<T> existsPredicate) {
 		BDD<T> bdd = transform(term);
-		if (!(existsPredicate == null)) {
+		if (existsPredicate != null) {
 			Set<T> variables = Terms.getVariables(term);
 			for (T variable : variables) {
 				if (existsPredicate.evaluate(variable)) {

src/main/java/org/jreliability/bdd/BDDTopEvent.java

@@ -21,10 +21,11 @@
 import org.apache.commons.collections15.Transformer;
 
 /**
- * The {@link BDDTopEvent} allows the fast calculation of the top event for a given {@link BDD}.
+ * The {@link BDDTopEvent} allows the fast calculation of the top event for a
+ * given {@link BDD}.
  * <p>
- * Here, the {@link BDD} is copied to an internal structure such that the {@link BDD#free()} method does not interfere
- * with this class.
+ * Here, the {@link BDD} is copied to an internal structure such that the
+ * {@link BDD#free()} method does not interfere with this class.
  * 
  * @author lukasiewycz
  * 
@@ -33,6 +34,31 @@
  */
 public class BDDTopEvent<T> {
 
+	/**
+	 * Map of the original variables to the internal structure of the variables.
+	 */
+	protected Map<T, Var> variables = new HashMap<>();
+
+	/**
+	 * A list of all variables nodes (ordered from bottom to the root).
+	 */
+	protected List<VarNode> nodes = new ArrayList<>();
+
+	/**
+	 * The instance of the zero node.
+	 */
+	protected Node zero = new NodeZero();
+
+	/**
+	 * The instance of the one node.
+	 */
+	protected Node one = new NodeOne();
+
+	/**
+	 * The root of the bdd.
+	 */
+	protected Node root;
+
 	/**
 	 * 
 	 * The {@link Var} is an internal variable class.
@@ -242,31 +268,6 @@ public double getValue() {
 		}
 	}
 
-	/**
-	 * Map of the original variables to the internal structure of the variables.
-	 */
-	Map<T, Var> variables = new HashMap<>();
-
-	/**
-	 * A list of all variables nodes (ordered from bottom to the root).
-	 */
-	List<VarNode> nodes = new ArrayList<>();
-
-	/**
-	 * The instance of the zero node.
-	 */
-	Node zero = new NodeZero();
-
-	/**
-	 * The instance of the one node.
-	 */
-	Node one = new NodeOne();
-
-	/**
-	 * The root of the bdd.
-	 */
-	Node root;
-
 	/**
 	 * Constructs the {@link BDDTopEvent} calculator for a given {@link BDD}.
 	 * 

src/main/java/org/jreliability/bdd/BDDs.java

@@ -352,14 +352,14 @@ protected static <T> BDD<T> buildConstraintBDD(List<Literal<T>> literals, int rh
 
 		Pair<Integer, Integer> key = new Pair<>(index, sum);
 		if (!memo.containsKey(key)) {
-			index--;
-			int coefficient = literals.get(index).getCoefficient();
-			materialLeft -= coefficient;
+			int newIndex = index - 1;
+			int coefficient = literals.get(newIndex).getCoefficient();
+			int newMaterialLeft = materialLeft - coefficient;
 			int hiSum = sum + coefficient;
 			int loSum = sum;
-			BDD<T> hiBDD = buildConstraintBDD(literals, rhs, index, hiSum, materialLeft, memo, provider);
-			BDD<T> loBDD = buildConstraintBDD(literals, rhs, index, loSum, materialLeft, memo, provider);
-			BDD<T> ifBDD = literals.get(index).getVariable();
+			BDD<T> hiBDD = buildConstraintBDD(literals, rhs, newIndex, hiSum, newMaterialLeft, memo, provider);
+			BDD<T> loBDD = buildConstraintBDD(literals, rhs, newIndex, loSum, newMaterialLeft, memo, provider);
+			BDD<T> ifBDD = literals.get(newIndex).getVariable();
 			BDD<T> resultBDD = ifBDD.ite(hiBDD, loBDD);
 			memo.put(key, resultBDD);
 		}

src/main/java/org/jreliability/bdd/javabdd/JBDD.java

@@ -32,9 +32,9 @@
  */
 public class JBDD<T> implements BDD<T> {
 
-	JBDDProvider<T> provider;
+	protected JBDDProvider<T> provider;
 
-	net.sf.javabdd.BDD bdd;
+	protected net.sf.javabdd.BDD bdd;
 
 	/**
 	 * The {@link AllSatIterator} is used as the {@link Iterator}.
@@ -44,7 +44,7 @@ public class JBDD<T> implements BDD<T> {
 	 */
 	private class AllSatIterator implements Iterator<BDD<T>> {
 
-		Iterator<T> iterator;
+		protected Iterator<T> iterator;
 
 		/**
 		 * Constructs a {@link Iterator} with a given JavaBDD JDD iterator.

src/main/java/org/jreliability/bdd/javabdd/JBDDProvider.java

@@ -97,6 +97,7 @@ public JBDDProvider(Type type, int vars, int variableGrowthFactor, int initialNu
 		default:
 			factory = JFactory.init(initialNumberofNodes, initialNumberofNodes);
 			factory.autoReorder(BDDFactory.REORDER_SIFT);
+			break;
 		}
 
 		factory.setVarNum(vars);

src/main/java/org/jreliability/booleanfunction/common/FALSETerm.java

@@ -22,14 +22,6 @@
  */
 public class FALSETerm implements Term {
 
-	/**
-	 * Constructs a {@link FALSETerm}.
-	 * 
-	 */
-	public FALSETerm() {
-		super();
-	}
-
 	/*
 	 * (non-Javadoc)
 	 * 

src/main/java/org/jreliability/booleanfunction/common/TRUETerm.java

@@ -22,14 +22,6 @@
  */
 public class TRUETerm implements Term {
 
-	/**
-	 * Constructs a {@link TRUETerm}.
-	 * 
-	 */
-	public TRUETerm() {
-		super();
-	}
-
 	/*
 	 * (non-Javadoc)
 	 * 

src/main/java/org/jreliability/common/Samples.java

@@ -24,11 +24,4 @@ public class Samples extends TreeMap<Double, Double> {
 
 	private static final long serialVersionUID = 1L;
 
-	/**
-	 * Constructs a {@link Samples}.
-	 */
-	public Samples() {
-		super();
-	}
-
 }