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

Packages that use MultipleAlignmentEnsemble

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

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

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

Modifier and Type	Class	Description
class	MultipleAlignmentEnsembleImpl	A general implementation of a MultipleAlignmentEnsemble.

Methods in org.biojava.nbio.structure.align.multiple that return MultipleAlignmentEnsemble

Modifier and Type	Method	Description
MultipleAlignmentEnsemble	MultipleAlignmentEnsemble.clone()	Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
MultipleAlignmentEnsemble	MultipleAlignment.getEnsemble()	Returns the parent Ensemble of the MultipleAlignment.
MultipleAlignmentEnsemble	MultipleAlignmentImpl.getEnsemble()

Methods in org.biojava.nbio.structure.align.multiple with parameters of type MultipleAlignmentEnsemble

Modifier and Type	Method	Description
void	MultipleAlignment.setEnsemble(MultipleAlignmentEnsemble parent)	Set the back-reference to its parent Ensemble.
void	MultipleAlignmentImpl.setEnsemble(MultipleAlignmentEnsemble parent)

Constructors in org.biojava.nbio.structure.align.multiple with parameters of type MultipleAlignmentEnsemble

Constructor	Description
MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble)	Constructor linking to an existing ensemble.

Uses of MultipleAlignmentEnsemble in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util with parameters of type MultipleAlignmentEnsemble

Modifier and Type	Method	Description
static String	MultipleAlignmentWriter.toXML(MultipleAlignmentEnsemble ensemble)	Converts all the information of a multiple alignment ensemble into an XML String format.

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

Methods in org.biojava.nbio.structure.align.xml that return MultipleAlignmentEnsemble

Modifier and Type	Method	Description
static MultipleAlignmentEnsemble	MultipleAlignmentXMLParser.parseEnsemble(Node root)

Methods in org.biojava.nbio.structure.align.xml that return types with arguments of type MultipleAlignmentEnsemble

Modifier and Type	Method	Description
static List<MultipleAlignmentEnsemble>	MultipleAlignmentXMLParser.parseXMLfile(String xml)	Creates a list of MultipleAlignment ensembles from an XML file.

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

Modifier and Type	Method	Description
static void	MultipleAlignmentXMLParser.parseHeader(Node node, MultipleAlignmentEnsemble ensemble)
static MultipleAlignment	MultipleAlignmentXMLParser.parseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble)
static void	MultipleAlignmentXMLParser.parseStructures(Node root, MultipleAlignmentEnsemble ensemble)
static void	MultipleAlignmentXMLConverter.printXMLensemble(PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble)
static void	MultipleAlignmentXMLConverter.printXMLheader(PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble)