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 |