CallableStructureAlignment (biojava-structure 7.0.0 API)

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

All Methods Instance Methods Concrete Methods
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 Detail
- 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 Detail

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)