Package org.biojava.nbio.structure.align
Class CallableStructureAlignment
java.lang.Object
org.biojava.nbio.structure.align.CallableStructureAlignment
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Constructor Summary
ConstructorsConstructorDescriptionDefault constructor.CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params) Constructor for all-to-all alignment calculation. -
Method Summary
Modifier and TypeMethodDescriptioncall()Atom[]getCa1()getCache()getPair()voidsetAlgorithmName(String algorithmName) voidvoidvoidsetOutFile(SynchronizedOutFile outFile) voidsetOutputDir(File outFileF) voidvoidsetParameters(ConfigStrucAligParams parameters)
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Constructor Details
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CallableStructureAlignment
public CallableStructureAlignment()Default constructor. Used in DB search. Instantiates an empty object, everything has to be set independently. -
CallableStructureAlignment
public CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params) Constructor for all-to-all alignment calculation. Used for MultipleMC seed alignment calculation, for example.- Parameters:
ca1- Atoms to align of the first structureca2- Atoms to align of the second structurealgorithmName- the pairwise aligner algorithm to use, a new instance will be created for each thread.params- parameter bean for the alignment.
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Method Details