Search Java Classes and Packages
#Org.biojava.nbio.structure.align.multiple Classes and Interfaces - 21 results found.
| Name | Description | Type | Package | Framework |
| AbstractScoresCache | Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| Block | A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockImpl | General implementation of a Block that supports any type of sequential alignment with gaps. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockSet | A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockSetImpl | A general implementation of a BlockSet to store a flexible part of a multiple alignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| CoreSuperimposer | Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignment | A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentDisplay | Utility functions to generalize the visualization of MultipleAlignments in molecular viewers. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentEnsemble | A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentEnsembleImpl | A general implementation of a MultipleAlignmentEnsemble. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentImpl | A general implementation of a MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentScorer | Utility class for calculating common scores of MultipleAlignments. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentTools | Utility functions for working with MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentWriter | This class contains functions for the conversion of MultipleAlignment to various String outputs. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleMcMain | Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleMcOptimizer | This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleMcParameters | Contains the parameters to be sent to the MC optimization. | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleStructureAligner | Interface for the Multiple Structure Alignment Algorithms. | Interface | org.biojava.nbio.structure.align | BioJava |
| MultipleSuperimposer | Interface for Multiple Alignment superposition algorithms. | Interface | org.biojava.nbio.structure.align.multiple.util | BioJava |
| ReferenceSuperimposer | Superimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in case | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| ScoresCache | Interface for classes which implement a temporary cache for various numeric scores, e. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |