org.biojava.nbio.structure.align

Class MultiThreadedDBSearch

java.lang.Object

org.biojava.nbio.structure.align.MultiThreadedDBSearch

public class MultiThreadedDBSearch
extends Object

Performs a multi threaded database search for an input protein structure

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)

Method Summary

Modifier and Type	Method and Description
void	cleanup()
StructureAlignment	getAlgorithm()
AtomCache	getAtomCache()
String	getCustomChain1()
String	getCustomFile1()
static String	getLegend(String algorithmName)
String	getOutFile()
File	getResultFile()
void	interrupt() stops what is currently happening and does not continue
void	run()
void	setAlgorithm(StructureAlignment algo)
void	setAtomCache(AtomCache cache)
void	setCustomChain1(String customChain1) sets a chain in a custom, user provided file
void	setCustomFile1(String customFile1) set the file path for a custom, user provided file, not a standard PDB file.
void	setOutFile(String outFile)
void	setResultFile(File resultList)

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiThreadedDBSearch

public MultiThreadedDBSearch(String name,
                             Structure structure,
                             String outFile,
                             StructureAlignment algorithm,
                             int nrCPUs,
                             boolean domainSplit)

Method Detail

getCustomFile1

public String getCustomFile1()

setCustomFile1

public void setCustomFile1(String customFile1)

set the file path for a custom, user provided file, not a standard PDB file.

Parameters:

customFile1 -

getCustomChain1

public String getCustomChain1()

setCustomChain1

public void setCustomChain1(String customChain1)

sets a chain in a custom, user provided file

Parameters:

customChain1 -

getAtomCache

public AtomCache getAtomCache()

setAtomCache

public void setAtomCache(AtomCache cache)

getAlgorithm

public StructureAlignment getAlgorithm()

setAlgorithm

public void setAlgorithm(StructureAlignment algo)

getOutFile

public String getOutFile()

setOutFile

public void setOutFile(String outFile)

getLegend

public static String getLegend(String algorithmName)

getResultFile

public File getResultFile()

setResultFile

public void setResultFile(File resultList)

run

public void run()

interrupt

public void interrupt()

stops what is currently happening and does not continue

cleanup

public void cleanup()