Package org.biojava.nbio.structure.align

Class CallableStructureAlignment

java.lang.Object

org.biojava.nbio.structure.align.CallableStructureAlignment

All Implemented Interfaces:

Callable<AFPChain>

public class CallableStructureAlignment
extends Object
implements Callable<AFPChain>

Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments). Adapted to a more general implementation since 4.1.0, because before it was thought for DB search only.

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
CallableStructureAlignment()	Default constructor.
CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params)	Constructor for all-to-all alignment calculation.

Method Summary

Modifier and Type	Method	Description
AFPChain	call()
Atom[]	getCa1()
AtomCache	getCache()
SynchronizedOutFile	getOutFile()
PdbPair	getPair()
void	setAlgorithmName(String algorithmName)
void	setCa1(Atom[] ca1)
void	setCache(AtomCache cache)
void	setOutFile(SynchronizedOutFile outFile)
void	setOutputDir(File outFileF)
void	setPair(PdbPair pair)
void	setParameters(ConfigStrucAligParams parameters)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

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 structure

ca2 - Atoms to align of the second structure

algorithmName - the pairwise aligner algorithm to use, a new instance will be created for each thread.

params - parameter bean for the alignment.

Method Details

call

public AFPChain call()
              throws Exception

Specified by:

call in interface Callable<AFPChain>

Throws:

Exception

getPair

public PdbPair getPair()

setPair

public void setPair(PdbPair pair)

getCache

public AtomCache getCache()

setCache

public void setCache(AtomCache cache)

getOutFile

public SynchronizedOutFile getOutFile()

setOutFile

public void setOutFile(SynchronizedOutFile outFile)

getCa1

public Atom[] getCa1()

setCa1

public void setCa1(Atom[] ca1)

setOutputDir

public void setOutputDir(File outFileF)

setAlgorithmName

public void setAlgorithmName(String algorithmName)

setParameters

public void setParameters(ConfigStrucAligParams parameters)