TreeChromosome.java

package net.bmahe.genetics4j.core.chromosomes;

import org.apache.commons.lang3.Validate;

/**
 * A chromosome implementation that represents genetic information as a tree structure.
 * 
 * <p>TreeChromosome is essential for genetic programming and other evolutionary approaches
 * that require hierarchical or nested representations. The tree structure allows for
 * variable-length solutions and naturally supports recursive data types and operations.
 * 
 * <p>This chromosome type is particularly suitable for:
 * <ul>
 * <li><strong>Genetic Programming</strong>: Evolving mathematical expressions, programs, and functions</li>
 * <li><strong>Decision trees</strong>: Classification and regression tree learning</li>
 * <li><strong>Parse trees</strong>: Grammar evolution and language processing</li>
 * <li><strong>Hierarchical structures</strong>: Neural network topologies, circuit designs</li>
 * <li><strong>Symbolic regression</strong>: Finding mathematical models that fit data</li>
 * <li><strong>Rule evolution</strong>: Evolving conditional logic and decision rules</li>
 * </ul>
 * 
 * <p>Key characteristics:
 * <ul>
 * <li><strong>Variable structure</strong>: Tree depth and branching can vary between individuals</li>
 * <li><strong>Hierarchical representation</strong>: Natural support for nested and recursive structures</li>
 * <li><strong>Type-safe nodes</strong>: Generic type parameter ensures consistent node data types</li>
 * <li><strong>Immutable backbone</strong>: Tree structure is fixed after construction</li>
 * </ul>
 * 
 * <p>The chromosome contains a single root node that represents the entire tree structure.
 * The tree size (total number of nodes) is calculated recursively from the root node.
 * For the purpose of the Chromosome interface, this counts as one "allele" since it
 * represents a single cohesive genetic unit.
 * 
 * <p>Tree genetic operators typically work by:
 * <ul>
 * <li><strong>Crossover</strong>: Exchanging subtrees between parent chromosomes</li>
 * <li><strong>Mutation</strong>: Replacing subtrees or individual nodes</li>
 * <li><strong>Growth/Pruning</strong>: Adding or removing branches to control complexity</li>
 * </ul>
 * 
 * @param <T> the type of data stored in tree nodes
 * @see TreeNode
 * @see Chromosome
 * @see TreeNode
 */
public class TreeChromosome<T> implements Chromosome {

	private final TreeNode<T> root;

	/**
	 * Creates a new tree chromosome with the specified root node.
	 * 
	 * @param _root the root node of the tree structure
	 * @throws IllegalArgumentException if root is null
	 */
	public TreeChromosome(final TreeNode<T> _root) {
		Validate.notNull(_root);

		this.root = _root;
	}

	/**
	 * Returns the number of alleles in this chromosome.
	 * 
	 * <p>For tree chromosomes, this always returns 1 since the entire tree
	 * is considered a single genetic unit (allele). To get the total number
	 * of nodes in the tree, use {@link #getSize()}.
	 * 
	 * @return 1, representing the tree as a single allele
	 */
	@Override
	public int getNumAlleles() {
		return 1;
	}

	/**
	 * Returns the root node of this tree chromosome.
	 * 
	 * @return the root node containing the entire tree structure
	 */
	public TreeNode<T> getRoot() {
		return root;
	}

	/**
	 * Returns the total number of nodes in the tree.
	 * 
	 * <p>This method recursively counts all nodes in the tree starting
	 * from the root node, including internal nodes and leaves.
	 * 
	 * @return the total number of nodes in the tree
	 */
	public int getSize() {
		return root.getSize();
	}

	@Override
	public int hashCode() {
		final int prime = 31;
		int result = 1;
		result = prime * result + ((root == null) ? 0 : root.hashCode());
		return result;
	}

	@Override
	public boolean equals(Object obj) {
		if (this == obj)
			return true;
		if (obj == null)
			return false;
		if (getClass() != obj.getClass())
			return false;
		TreeChromosome other = (TreeChromosome) obj;
		if (root == null) {
			if (other.root != null)
				return false;
		} else if (!root.equals(other.root))
			return false;
		return true;
	}

	@Override
	public String toString() {
		return "TreeChromosome [root=" + root + "]";
	}
}























Active mutators

CONDITIONALS_BOUNDARY
CONSTRUCTOR_CALLS
EMPTY_RETURNS
EXPERIMENTAL_ARGUMENT_PROPAGATION
EXPERIMENTAL_BIG_DECIMAL
EXPERIMENTAL_BIG_INTEGER
EXPERIMENTAL_MEMBER_VARIABLE
EXPERIMENTAL_NAKED_RECEIVER
EXPERIMENTAL_REMOVE_SWITCH_MUTATOR_[0-99]
EXPERIMENTAL_SWITCH
FALSE_RETURNS
INCREMENTS
INLINE_CONSTS
INVERT_NEGS
MATH
NEGATE_CONDITIONALS
NON_VOID_METHOD_CALLS
NULL_RETURNS
PRIMITIVE_RETURNS
REMOVE_CONDITIONALS_EQUAL_ELSE
REMOVE_CONDITIONALS_EQUAL_IF
REMOVE_CONDITIONALS_ORDER_ELSE
REMOVE_CONDITIONALS_ORDER_IF
REMOVE_INCREMENTS
TRUE_RETURNS
VOID_METHOD_CALLS

Tests examined

net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] (7 ms)

Report generated by PIT 1.19.6

1		package net.bmahe.genetics4j.core.chromosomes;
2
3		import org.apache.commons.lang3.Validate;
4
5		/**
6		* A chromosome implementation that represents genetic information as a tree structure.
7		*
8		* <p>TreeChromosome is essential for genetic programming and other evolutionary approaches
9		* that require hierarchical or nested representations. The tree structure allows for
10		* variable-length solutions and naturally supports recursive data types and operations.
11		*
12		* <p>This chromosome type is particularly suitable for:
13		* <ul>
14		* <li><strong>Genetic Programming</strong>: Evolving mathematical expressions, programs, and functions</li>
15		* <li><strong>Decision trees</strong>: Classification and regression tree learning</li>
16		* <li><strong>Parse trees</strong>: Grammar evolution and language processing</li>
17		* <li><strong>Hierarchical structures</strong>: Neural network topologies, circuit designs</li>
18		* <li><strong>Symbolic regression</strong>: Finding mathematical models that fit data</li>
19		* <li><strong>Rule evolution</strong>: Evolving conditional logic and decision rules</li>
20		* </ul>
21		*
22		* <p>Key characteristics:
23		* <ul>
24		* <li><strong>Variable structure</strong>: Tree depth and branching can vary between individuals</li>
25		* <li><strong>Hierarchical representation</strong>: Natural support for nested and recursive structures</li>
26		* <li><strong>Type-safe nodes</strong>: Generic type parameter ensures consistent node data types</li>
27		* <li><strong>Immutable backbone</strong>: Tree structure is fixed after construction</li>
28		* </ul>
29		*
30		* <p>The chromosome contains a single root node that represents the entire tree structure.
31		* The tree size (total number of nodes) is calculated recursively from the root node.
32		* For the purpose of the Chromosome interface, this counts as one "allele" since it
33		* represents a single cohesive genetic unit.
34		*
35		* <p>Tree genetic operators typically work by:
36		* <ul>
37		* <li><strong>Crossover</strong>: Exchanging subtrees between parent chromosomes</li>
38		* <li><strong>Mutation</strong>: Replacing subtrees or individual nodes</li>
39		* <li><strong>Growth/Pruning</strong>: Adding or removing branches to control complexity</li>
40		* </ul>
41		*
42		* @param <T> the type of data stored in tree nodes
43		* @see TreeNode
44		* @see Chromosome
45		* @see TreeNode
46		*/
47		public class TreeChromosome<T> implements Chromosome {
48
49		private final TreeNode<T> root;
50
51		/**
52		* Creates a new tree chromosome with the specified root node.
53		*
54		* @param _root the root node of the tree structure
55		* @throws IllegalArgumentException if root is null
56		*/
57		public TreeChromosome(final TreeNode<T> _root) {
58		Validate.notNull(_root);
59
60	1 1. <init> : Removed assignment to member variable root → KILLED	this.root = _root;
61		}
62
63		/**
64		* Returns the number of alleles in this chromosome.
65		*
66		* <p>For tree chromosomes, this always returns 1 since the entire tree
67		* is considered a single genetic unit (allele). To get the total number
68		* of nodes in the tree, use {@link #getSize()}.
69		*
70		* @return 1, representing the tree as a single allele
71		*/
72		@Override
73		public int getNumAlleles() {
74	2 1. getNumAlleles : Substituted 1 with 0 → KILLED 2. getNumAlleles : replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getNumAlleles → KILLED	return 1;
75		}
76
77		/**
78		* Returns the root node of this tree chromosome.
79		*
80		* @return the root node containing the entire tree structure
81		*/
82		public TreeNode<T> getRoot() {
83	1 1. getRoot : replaced return value with null for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getRoot → KILLED	return root;
84		}
85
86		/**
87		* Returns the total number of nodes in the tree.
88		*
89		* <p>This method recursively counts all nodes in the tree starting
90		* from the root node, including internal nodes and leaves.
91		*
92		* @return the total number of nodes in the tree
93		*/
94		public int getSize() {
95	2 1. getSize : replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getSize → KILLED 2. getSize : removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::getSize → KILLED	return root.getSize();
96		}
97
98		@Override
99		public int hashCode() {
100	1 1. hashCode : Substituted 31 with 32 → NO_COVERAGE	final int prime = 31;
101	1 1. hashCode : Substituted 1 with 0 → NO_COVERAGE	int result = 1;
102	8 1. hashCode : Substituted 0 with 1 → NO_COVERAGE 2. hashCode : removed conditional - replaced equality check with true → NO_COVERAGE 3. hashCode : negated conditional → NO_COVERAGE 4. hashCode : Replaced integer addition with subtraction → NO_COVERAGE 5. hashCode : Substituted 31 with 32 → NO_COVERAGE 6. hashCode : Replaced integer multiplication with division → NO_COVERAGE 7. hashCode : removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::hashCode → NO_COVERAGE 8. hashCode : removed conditional - replaced equality check with false → NO_COVERAGE	result = prime * result + ((root == null) ? 0 : root.hashCode());
103	1 1. hashCode : replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::hashCode → NO_COVERAGE	return result;
104		}
105
106		@Override
107		public boolean equals(Object obj) {
108	2 1. equals : removed conditional - replaced equality check with true → NO_COVERAGE 2. equals : negated conditional → NO_COVERAGE	if (this == obj)
109	2 1. equals : Substituted 1 with 0 → NO_COVERAGE 2. equals : replaced boolean return with false for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE	return true;
110	3 1. equals : negated conditional → NO_COVERAGE 2. equals : removed conditional - replaced equality check with true → NO_COVERAGE 3. equals : removed conditional - replaced equality check with false → NO_COVERAGE	if (obj == null)
111	2 1. equals : replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2. equals : Substituted 0 with 1 → NO_COVERAGE	return false;
112	5 1. equals : negated conditional → NO_COVERAGE 2. equals : removed conditional - replaced equality check with false → NO_COVERAGE 3. equals : removed call to java/lang/Object::getClass → NO_COVERAGE 4. equals : removed conditional - replaced equality check with true → NO_COVERAGE 5. equals : removed call to java/lang/Object::getClass → NO_COVERAGE	if (getClass() != obj.getClass())
113	2 1. equals : replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2. equals : Substituted 0 with 1 → NO_COVERAGE	return false;
114		TreeChromosome other = (TreeChromosome) obj;
115	3 1. equals : removed conditional - replaced equality check with true → NO_COVERAGE 2. equals : removed conditional - replaced equality check with false → NO_COVERAGE 3. equals : negated conditional → NO_COVERAGE	if (root == null) {
116	3 1. equals : removed conditional - replaced equality check with false → NO_COVERAGE 2. equals : removed conditional - replaced equality check with true → NO_COVERAGE 3. equals : negated conditional → NO_COVERAGE	if (other.root != null)
117	2 1. equals : replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2. equals : Substituted 0 with 1 → NO_COVERAGE	return false;
118	4 1. equals : negated conditional → NO_COVERAGE 2. equals : removed conditional - replaced equality check with false → NO_COVERAGE 3. equals : removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::equals → NO_COVERAGE 4. equals : removed conditional - replaced equality check with true → NO_COVERAGE	} else if (!root.equals(other.root))
119	2 1. equals : replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2. equals : Substituted 0 with 1 → NO_COVERAGE	return false;
120	2 1. equals : replaced boolean return with false for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2. equals : Substituted 1 with 0 → NO_COVERAGE	return true;
121		}
122
123		@Override
124		public String toString() {
125	2 1. toString : replaced return value with "" for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::toString → NO_COVERAGE 2. toString : removed call to java/lang/String::valueOf → NO_COVERAGE	return "TreeChromosome [root=" + root + "]";
126		}
127		}
		Mutations
60		1.1 Location : <init> Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] Removed assignment to member variable root → KILLED
74		1.1 Location : getNumAlleles Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] Substituted 1 with 0 → KILLED 2.2 Location : getNumAlleles Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getNumAlleles → KILLED
83		1.1 Location : getRoot Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] replaced return value with null for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getRoot → KILLED
95		1.1 Location : getSize Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getSize → KILLED 2.2 Location : getSize Killed by : net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.core.chromosomes.TreeChromosomeTest]/[method:simple()] removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::getSize → KILLED
100		1.1 Location : hashCode Killed by : none Substituted 31 with 32 → NO_COVERAGE
101		1.1 Location : hashCode Killed by : none Substituted 1 with 0 → NO_COVERAGE
102		1.1 Location : hashCode Killed by : none Substituted 0 with 1 → NO_COVERAGE 2.2 Location : hashCode Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 3.3 Location : hashCode Killed by : none negated conditional → NO_COVERAGE 4.4 Location : hashCode Killed by : none Replaced integer addition with subtraction → NO_COVERAGE 5.5 Location : hashCode Killed by : none Substituted 31 with 32 → NO_COVERAGE 6.6 Location : hashCode Killed by : none Replaced integer multiplication with division → NO_COVERAGE 7.7 Location : hashCode Killed by : none removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::hashCode → NO_COVERAGE 8.8 Location : hashCode Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE
103		1.1 Location : hashCode Killed by : none replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::hashCode → NO_COVERAGE
108		1.1 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 2.2 Location : equals Killed by : none negated conditional → NO_COVERAGE
109		1.1 Location : equals Killed by : none Substituted 1 with 0 → NO_COVERAGE 2.2 Location : equals Killed by : none replaced boolean return with false for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE
110		1.1 Location : equals Killed by : none negated conditional → NO_COVERAGE 2.2 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 3.3 Location : equals Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE
111		1.1 Location : equals Killed by : none replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2.2 Location : equals Killed by : none Substituted 0 with 1 → NO_COVERAGE
112		1.1 Location : equals Killed by : none negated conditional → NO_COVERAGE 2.2 Location : equals Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE 3.3 Location : equals Killed by : none removed call to java/lang/Object::getClass → NO_COVERAGE 4.4 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 5.5 Location : equals Killed by : none removed call to java/lang/Object::getClass → NO_COVERAGE
113		1.1 Location : equals Killed by : none replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2.2 Location : equals Killed by : none Substituted 0 with 1 → NO_COVERAGE
115		1.1 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 2.2 Location : equals Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE 3.3 Location : equals Killed by : none negated conditional → NO_COVERAGE
116		1.1 Location : equals Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE 2.2 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE 3.3 Location : equals Killed by : none negated conditional → NO_COVERAGE
117		1.1 Location : equals Killed by : none replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2.2 Location : equals Killed by : none Substituted 0 with 1 → NO_COVERAGE
118		1.1 Location : equals Killed by : none negated conditional → NO_COVERAGE 2.2 Location : equals Killed by : none removed conditional - replaced equality check with false → NO_COVERAGE 3.3 Location : equals Killed by : none removed call to net/bmahe/genetics4j/core/chromosomes/TreeNode::equals → NO_COVERAGE 4.4 Location : equals Killed by : none removed conditional - replaced equality check with true → NO_COVERAGE
119		1.1 Location : equals Killed by : none replaced boolean return with true for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2.2 Location : equals Killed by : none Substituted 0 with 1 → NO_COVERAGE
120		1.1 Location : equals Killed by : none replaced boolean return with false for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::equals → NO_COVERAGE 2.2 Location : equals Killed by : none Substituted 1 with 0 → NO_COVERAGE
125		1.1 Location : toString Killed by : none replaced return value with "" for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::toString → NO_COVERAGE 2.2 Location : toString Killed by : none removed call to java/lang/String::valueOf → NO_COVERAGE

TreeChromosome.java

Mutations

Active mutators

Tests examined