Uses of Package
org.biojava.nbio.structure.align.ce

Packages that use org.biojava.nbio.structure.align.ce

Package	Description
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.fatcat	Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align

Class and Description
ConfigStrucAligParams

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.ce

Class and Description
AbstractUserArgumentProcessor Base class for a new structure alignment CLI.
CECalculator This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCPMain.CPRange Tiny wrapper for the disallowed regions of an alignment.
CECPParameters Provides parameters to CeCPMain
CECPParameters.DuplicationHint
CeMain The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeParameters Contains the parameters that can be sent to CE
CeParameters.ScoringStrategy
CeUserArgumentProcessor process the arguments from command line
CeUserArgumentProcessor.CeStartupParams
ConfigStrucAligParams
MatrixListener
OptimalCECPParameters Contains the parameters that can be sent to CE
StartupParameters a simple bean that contains the parameters that can get set at startup
UserArgumentProcessor

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.fatcat

Class and Description
AbstractUserArgumentProcessor Base class for a new structure alignment CLI.
ConfigStrucAligParams
StartupParameters a simple bean that contains the parameters that can get set at startup
UserArgumentProcessor

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.fatcat.calc

Class and Description
ConfigStrucAligParams

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.gui

Class and Description
ConfigStrucAligParams

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.multiple.mc

Class and Description
ConfigStrucAligParams

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.seq

Class and Description
AbstractUserArgumentProcessor Base class for a new structure alignment CLI.
ConfigStrucAligParams
StartupParameters a simple bean that contains the parameters that can get set at startup
UserArgumentProcessor

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.align.util

Class and Description
StartupParameters a simple bean that contains the parameters that can get set at startup

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.symmetry.internal

Class and Description
CeParameters Contains the parameters that can be sent to CE
ConfigStrucAligParams

Classes in org.biojava.nbio.structure.align.ce used by org.biojava.nbio.structure.symmetry.utils

Class and Description
CECalculator This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.