- Generated by
1.9.4
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DENOPTIM
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Types of mutation defined in relation to what happens to the target vertex (i.e., the actual mutation site), and the child vertices, i.e., any vertices reachable by a directed path from the target vertex. More...
Public Attributes | |
| DELETE | |
| Removes the target vertex and all child vertices. More... | |
| EXTEND | |
| append vertices on the target vertex according to substitution probability. More... | |
| CHANGEBRANCH | |
| Replace the target vertex and any of the child vertices. More... | |
| CHANGELINK | |
| Replace the target vertex keeping all the child structure. More... | |
| ADDLINK | |
| Adds a vertex between two previously connected vertexes. More... | |
| ADDRING | |
| Creates a ring-closure to add a ring. More... | |
| DELETELINK | |
| Removes a vertex from a tree and merges remaining branches into the remaining trunk. More... | |
| DELETECHAIN | |
| Removes a vertex and all its neighbors recursively until a branching point, i.e., until a vertex that is connected to more than two non-capping vertexes. More... | |
Types of mutation defined in relation to what happens to the target vertex (i.e., the actual mutation site), and the child vertices, i.e., any vertices reachable by a directed path from the target vertex.
Definition at line 27 of file MutationType.java.
| denoptim.utils.MutationType.ADDLINK |
Adds a vertex between two previously connected vertexes.
Definition at line 54 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), denoptim.graph.Template.getMutationTypes(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
| denoptim.utils.MutationType.ADDRING |
Creates a ring-closure to add a ring.
Definition at line 59 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), and denoptim.programs.denovo.GAParameters.processParameters().
| denoptim.utils.MutationType.CHANGEBRANCH |
Replace the target vertex and any of the child vertices.
The effect on the child vertices is decided by substitution probability.
Definition at line 44 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), denoptim.json.DENOPTIMgsonTest.testTemplateSerialization(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
| denoptim.utils.MutationType.CHANGELINK |
Replace the target vertex keeping all the child structure.
Definition at line 49 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), denoptim.graph.Template.getMutationTypes(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), and denoptim.json.DENOPTIMgsonTest.testTemplateSerialization().
| denoptim.utils.MutationType.DELETE |
Removes the target vertex and all child vertices.
Definition at line 32 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
| denoptim.utils.MutationType.DELETECHAIN |
Removes a vertex and all its neighbors recursively until a branching point, i.e., until a vertex that is connected to more than two non-capping vertexes.
Definition at line 74 of file MutationType.java.
Referenced by denoptim.ga.GraphOperations.deleteChain(), denoptim.graph.Vertex.getMutationTypes(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
| denoptim.utils.MutationType.DELETELINK |
Removes a vertex from a tree and merges remaining branches into the remaining trunk.
Definition at line 65 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
| denoptim.utils.MutationType.EXTEND |
append vertices on the target vertex according to substitution probability.
Definition at line 38 of file MutationType.java.
Referenced by denoptim.graph.Vertex.getMutationTypes(), denoptim.graph.Template.getMutationTypes(), denoptim.graph.VertexTest.testGetMutationSites(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().
1.9.4