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#Org.biojava.nbio.structure.align.multiple Classes and Interfaces - 21 results found.
NameDescriptionTypePackageFramework
AbstractScoresCacheAbstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.Classorg.biojava.nbio.structure.align.multipleBioJava
BlockA Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in aInterfaceorg.biojava.nbio.structure.align.multipleBioJava
BlockImplGeneral implementation of a Block that supports any type of sequential alignment with gaps.Classorg.biojava.nbio.structure.align.multipleBioJava
BlockSetA BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.Interfaceorg.biojava.nbio.structure.align.multipleBioJava
BlockSetImplA general implementation of a BlockSet to store a flexible part of a multiple alignment.Classorg.biojava.nbio.structure.align.multipleBioJava
CoreSuperimposerSuperimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentA MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.Interfaceorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentDisplayUtility functions to generalize the visualization of MultipleAlignments in molecular viewers.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentEnsembleA MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm,Interfaceorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentEnsembleImplA general implementation of a MultipleAlignmentEnsemble.Classorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentImplA general implementation of a MultipleAlignment.Classorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentScorerUtility class for calculating common scores of MultipleAlignments.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentToolsUtility functions for working with MultipleAlignment.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentWriterThis class contains functions for the conversion of MultipleAlignment to various String outputs.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleMcMainMain class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm,Classorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleMcOptimizerThis class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlightClassorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleMcParametersContains the parameters to be sent to the MC optimization.Classorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleStructureAlignerInterface for the Multiple Structure Alignment Algorithms.Interfaceorg.biojava.nbio.structure.alignBioJava
MultipleSuperimposerInterface for Multiple Alignment superposition algorithms.Interfaceorg.biojava.nbio.structure.align.multiple.utilBioJava
ReferenceSuperimposerSuperimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in caseClassorg.biojava.nbio.structure.align.multiple.utilBioJava
ScoresCacheInterface for classes which implement a temporary cache for various numeric scores, e.Interfaceorg.biojava.nbio.structure.align.multipleBioJava