Package org.biojava.nbio.structure.align
Class MultiThreadedDBSearch
- java.lang.Object
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- org.biojava.nbio.structure.align.MultiThreadedDBSearch
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public class MultiThreadedDBSearch extends Object
Performs a multi threaded database search for an input protein structure- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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 continuevoid
run()
void
setAlgorithm(StructureAlignment algo)
void
setAtomCache(AtomCache cache)
void
setCustomChain1(String customChain1)
sets a chain in a custom, user provided filevoid
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)
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Constructor Detail
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MultiThreadedDBSearch
public MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)
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Method Detail
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getCustomFile1
public String getCustomFile1()
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setCustomFile1
public void setCustomFile1(String customFile1)
set the file path for a custom, user provided file, not a standard PDB file.- Parameters:
customFile1
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getCustomChain1
public String getCustomChain1()
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setCustomChain1
public void setCustomChain1(String customChain1)
sets a chain in a custom, user provided file- Parameters:
customChain1
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getAtomCache
public AtomCache getAtomCache()
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setAtomCache
public void setAtomCache(AtomCache cache)
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getAlgorithm
public StructureAlignment getAlgorithm()
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setAlgorithm
public void setAlgorithm(StructureAlignment algo)
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getOutFile
public String getOutFile()
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setOutFile
public void setOutFile(String outFile)
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getResultFile
public File getResultFile()
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setResultFile
public void setResultFile(File resultList)
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run
public void run()
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interrupt
public void interrupt()
stops what is currently happening and does not continue
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cleanup
public void cleanup()
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