Package edu.mssm.crover.representation

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.
Extended_ColorAnnotation
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.
SequenceTest	Testing edu.mssm.crover.representation.Sequence.
Spacer_Annotation	Annotates N and C term spacers for use in drawing RbDg diagrams.
TM_Annotation	Annotates parts of transmembrane domains.
TmDomain_Annotation	Annotates a whole trans-membrane domain.
URL_Annotation

Exception Summary

InvalidLocationException
NoSuchResidue