| 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 that require hierarchical or | |
| 9 | * nested representations. The tree structure allows for variable-length solutions and naturally supports recursive data | |
| 10 | * 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. The tree size (total number | |
| 31 | * of nodes) is calculated recursively from the root node. For the purpose of the Chromosome interface, this counts as | |
| 32 | * one "allele" since it represents a single cohesive genetic unit. | |
| 33 | * | |
| 34 | * <p>Tree genetic operators typically work by: | |
| 35 | * <ul> | |
| 36 | * <li><strong>Crossover</strong>: Exchanging subtrees between parent chromosomes</li> | |
| 37 | * <li><strong>Mutation</strong>: Replacing subtrees or individual nodes</li> | |
| 38 | * <li><strong>Growth/Pruning</strong>: Adding or removing branches to control complexity</li> | |
| 39 | * </ul> | |
| 40 | * | |
| 41 | * @param <T> the type of data stored in tree nodes | |
| 42 | * @see TreeNode | |
| 43 | * @see Chromosome | |
| 44 | * @see TreeNode | |
| 45 | */ | |
| 46 | public class TreeChromosome<T> implements Chromosome { | |
| 47 | ||
| 48 | private final TreeNode<T> root; | |
| 49 | ||
| 50 | /** | |
| 51 | * Creates a new tree chromosome with the specified root node. | |
| 52 | * | |
| 53 | * @param _root the root node of the tree structure | |
| 54 | * @throws IllegalArgumentException if root is null | |
| 55 | */ | |
| 56 | public TreeChromosome(final TreeNode<T> _root) { | |
| 57 | Validate.notNull(_root); | |
| 58 | ||
| 59 |
1
1. <init> : Removed assignment to member variable root → KILLED |
this.root = _root; |
| 60 | } | |
| 61 | ||
| 62 | /** | |
| 63 | * Returns the number of alleles in this chromosome. | |
| 64 | * | |
| 65 | * <p>For tree chromosomes, this always returns 1 since the entire tree is considered a single genetic unit (allele). | |
| 66 | * To get the total number of nodes in the tree, use {@link #getSize()}. | |
| 67 | * | |
| 68 | * @return 1, representing the tree as a single allele | |
| 69 | */ | |
| 70 | @Override | |
| 71 | public int getNumAlleles() { | |
| 72 |
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; |
| 73 | } | |
| 74 | ||
| 75 | /** | |
| 76 | * Returns the root node of this tree chromosome. | |
| 77 | * | |
| 78 | * @return the root node containing the entire tree structure | |
| 79 | */ | |
| 80 | public TreeNode<T> getRoot() { | |
| 81 |
1
1. getRoot : replaced return value with null for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::getRoot → KILLED |
return root; |
| 82 | } | |
| 83 | ||
| 84 | /** | |
| 85 | * Returns the total number of nodes in the tree. | |
| 86 | * | |
| 87 | * <p>This method recursively counts all nodes in the tree starting from the root node, including internal nodes and | |
| 88 | * leaves. | |
| 89 | * | |
| 90 | * @return the total number of nodes in the tree | |
| 91 | */ | |
| 92 | public int getSize() { | |
| 93 |
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(); |
| 94 | } | |
| 95 | ||
| 96 | @Override | |
| 97 | public int hashCode() { | |
| 98 |
1
1. hashCode : Substituted 31 with 32 → NO_COVERAGE |
final int prime = 31; |
| 99 |
1
1. hashCode : Substituted 1 with 0 → NO_COVERAGE |
int result = 1; |
| 100 |
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()); |
| 101 |
1
1. hashCode : replaced int return with 0 for net/bmahe/genetics4j/core/chromosomes/TreeChromosome::hashCode → NO_COVERAGE |
return result; |
| 102 | } | |
| 103 | ||
| 104 | @Override | |
| 105 | public boolean equals(Object obj) { | |
| 106 |
2
1. equals : removed conditional - replaced equality check with true → NO_COVERAGE 2. equals : negated conditional → NO_COVERAGE |
if (this == obj) |
| 107 |
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; |
| 108 |
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) |
| 109 |
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; |
| 110 |
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()) |
| 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 | TreeChromosome other = (TreeChromosome) obj; | |
| 113 |
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) { |
| 114 |
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) |
| 115 |
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; |
| 116 |
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)) |
| 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 |
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; |
| 119 | } | |
| 120 | ||
| 121 | @Override | |
| 122 | public String toString() { | |
| 123 |
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 + "]"; |
| 124 | } | |
| 125 | } | |
Mutations | ||
| 59 |
1.1 |
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| 72 |
1.1 2.2 |
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| 81 |
1.1 |
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| 93 |
1.1 2.2 |
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| 98 |
1.1 |
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| 99 |
1.1 |
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| 100 |
1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8 |
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| 101 |
1.1 |
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| 106 |
1.1 2.2 |
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| 107 |
1.1 2.2 |
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| 108 |
1.1 2.2 3.3 |
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| 109 |
1.1 2.2 |
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| 110 |
1.1 2.2 3.3 4.4 5.5 |
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| 111 |
1.1 2.2 |
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| 113 |
1.1 2.2 3.3 |
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| 114 |
1.1 2.2 3.3 |
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| 115 |
1.1 2.2 |
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| 116 |
1.1 2.2 3.3 4.4 |
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| 117 |
1.1 2.2 |
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| 118 |
1.1 2.2 |
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| 123 |
1.1 2.2 |