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

Packages that use Block

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

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

Modifier and Type	Class and Description
class	BlockImpl General implementation of a Block that supports any type of sequential alignment with gaps.

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

Modifier and Type	Method and Description
Block	Block.clone() Creates and returns an identical copy of this block.
Block	BlockImpl.clone()
Block	MultipleAlignment.getBlock(int index) Returns the Block with the specified index of the MultipleAlignment.
Block	MultipleAlignmentImpl.getBlock(int index)

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

Modifier and Type	Method and Description
List<Block>	MultipleAlignment.getBlocks() Convenience method to get a List of all Blocks from all BlockSets.
List<Block>	MultipleAlignmentImpl.getBlocks()
List<Block>	BlockSetImpl.getBlocks()
List<Block>	BlockSet.getBlocks() Returns the List of alignment Blocks of the BlockSet.

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

Modifier and Type	Method and Description
void	BlockSetImpl.setBlocks(List<Block> blocks)
void	BlockSet.setBlocks(List<Block> blocks) Set the List of alignment Blocks of the BlockSet.

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

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

Modifier and Type	Method and Description
static List<Integer>	MultipleAlignmentTools.getCorePositions(Block block) Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.

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

Modifier and Type	Method and Description
static void	MultipleAlignmentTools.sortBlocks(List<Block> blocks, int sortedIndex) Sort blocks so that the specified row is in sequential order.

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

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

Modifier and Type	Method and Description
static Block	MultipleAlignmentXMLParser.parseBlock(Node root, BlockSet blockSet)

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

Modifier and Type	Method and Description
static void	MultipleAlignmentXMLConverter.printXMLblock(PrettyXMLWriter xml, Block b)