Package edu.mssm.crover.representation

Provides for the representation of biological objects.


Interface Summary
AnnotatedBioSequence A BiologicalSequence with annotations.
AnnotationSupport Interface that supports annotations.
BiologicalAlignment Interface to represent a biological alignment of protein sequences.
BiologicalAnnotation Represents a single annotation.
BiologicalAnnotations Extendable annotation support for AnnotatedBioSequence objects.
BiologicalDescription This interface is not specified.
BiologicalOrigin Represents the origin of an information.
BiologicalSequence Interface to a represent a biological protein sequence.
Description Not specified.
RootObject Switch for CORBA support.

Class Summary
Alignment Default implementation of BiologicalAlignment.
Annotation Default implementation of BiologicaAnnotation.
Annotations Default implementation of BiologicalAnnotations.
Color_Annotation Colors groups of residues according to a property.
Disulfide_Annotation Annotates disulfide bridges.
Domain_Annotation Annotates protein domains.
ExtendedSS_Annotation Annotates secondary structure elements.
Mutation_Annotation Annotates ponctual mutations.
Origin Default implementation of BiologicalOrigin.
OriginFactory Factory to return origins of a specific kind.
RandomAccessAlignment RandomAccessAlignment proposes an implementation of a random access alignment data storage.
ResidueAnnotation Flag residues in a sequence.
SecondaryStructure_Annotation Annotates secondary structure elements.
Sequence Default implementation of BiologicalSequence.
SequenceOrigin_Annotation This annotation describes the origin of the sequence itself.
TM_Annotation Annotates parts of transmembrane domains.
TmDomain_Annotation Annotates a whole trans-membrane domain.

Exception Summary

Package edu.mssm.crover.representation Description

Provides for the representation of biological objects. The word representation refers to a model of information (specified via interfaces) and to a storage component (default implementations for the interfaces).

Package Specification

Related Documentation

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