Uses of Interface
org.biojava.nbio.structure.align.multiple.ScoresCache

Packages that use ScoresCache

Package	Description
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.xml	Serialization and deserialization for structure alignment results (as AFPChain object) to XML.

Uses of ScoresCache in org.biojava.nbio.structure.align.multiple

Subinterfaces of ScoresCache in org.biojava.nbio.structure.align.multiple

Modifier and Type	Interface and Description
interface	Block A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
interface	BlockSet A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
interface	MultipleAlignment A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
interface	MultipleAlignmentEnsemble A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).

Classes in org.biojava.nbio.structure.align.multiple that implement ScoresCache

Modifier and Type	Class and Description
class	AbstractScoresCache Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
class	BlockImpl General implementation of a Block that supports any type of sequential alignment with gaps.
class	BlockSetImpl A general implementation of a BlockSet to store a flexible part of a multiple alignment.
class	MultipleAlignmentEnsembleImpl A general implementation of a MultipleAlignmentEnsemble.
class	MultipleAlignmentImpl A general implementation of a MultipleAlignment.

Uses of ScoresCache in org.biojava.nbio.structure.align.xml

Methods in org.biojava.nbio.structure.align.xml with parameters of type ScoresCache

Modifier and Type	Method and Description
static void	MultipleAlignmentXMLParser.parseScoresCache(Node root, ScoresCache cache)
static void	MultipleAlignmentXMLConverter.printXMLscoresCache(PrettyXMLWriter xml, ScoresCache cache)