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

Packages that use BlockSet

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 BlockSet in org.biojava.nbio.structure.align.multiple

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

Modifier and Type	Class and Description
class	BlockSetImpl A general implementation of a BlockSet to store a flexible part of a multiple alignment.

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

Modifier and Type	Method and Description
BlockSet	BlockSet.clone() Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
BlockSet	BlockImpl.getBlockSet()
BlockSet	Block.getBlockSet() Returns the parent BlockSet of the Block.
BlockSet	MultipleAlignmentImpl.getBlockSet(int index)
BlockSet	MultipleAlignment.getBlockSet(int index) Returns the BlockSet with the specified index of the MultipleAlignment.

Methods in org.biojava.nbio.structure.align.multiple that return types with arguments of type BlockSet

Modifier and Type	Method and Description
List<BlockSet>	MultipleAlignmentImpl.getBlockSets()
List<BlockSet>	MultipleAlignment.getBlockSets() Returns the BlockSet List of the multiple structure alignment.

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

Modifier and Type	Method and Description
void	BlockImpl.setBlockSet(BlockSet parent)
void	Block.setBlockSet(BlockSet parent) Set the back-reference to its parent BlockSet.

Method parameters in org.biojava.nbio.structure.align.multiple with type arguments of type BlockSet

Modifier and Type	Method and Description
void	MultipleAlignmentImpl.setBlockSets(List<BlockSet> blockSets)
void	MultipleAlignment.setBlockSets(List<BlockSet> blockSets) Sets the List of BlockSet List of the specified alignment.

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

Constructor and Description
BlockImpl(BlockSet blockSet) Constructor.

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

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

Modifier and Type	Method and Description
static BlockSet	MultipleAlignmentXMLParser.parseBlockSet(Node root, MultipleAlignment msa)

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

Modifier and Type	Method and Description
static Block	MultipleAlignmentXMLParser.parseBlock(Node root, BlockSet blockSet)
static void	MultipleAlignmentXMLConverter.printXMLblockSet(PrettyXMLWriter xml, BlockSet bs)