StructureAlignment (biojava 6.1.0 API)

All Known Implementing Classes:

AbstractStructureAlignment, BioJavaStructureAlignment, CeCPMain, CeMain, CeSideChainMain, FatCatFlexible, FatCatRigid, OptimalCECPMain, SmithWaterman3Daligner
```
public interface StructureAlignment
```

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`AFPChain`	`align(Atom[] ca1, Atom[] ca2)`	Run an alignment while specifying the atoms to be aligned.
`AFPChain`	`align(Atom[] ca1, Atom[] ca2, Object params)`	run an alignment and also send a bean containing the parameters.
`String`	`getAlgorithmName()`	Get the name of the Algorithm
`ConfigStrucAligParams`	`getParameters()`	Return the paramers for this algorithm.
`String`	`getVersion()`	Get the Version information for this Algorithm.
`void`	`setParameters(ConfigStrucAligParams parameters)`	Set the default parameters for this algorithm to use

- Method Detail
  - align
```
AFPChain align(Atom[] ca1,
               Atom[] ca2)
        throws StructureException
```
    Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.
    
    Parameters:
    
    ca1 -
    
    ca2 -
    
    Returns:
    
    the afpChain object that contains the alignment.
    
    Throws:
    
    StructureException
  - align
```
AFPChain align(Atom[] ca1,
               Atom[] ca2,
               Object params)
        throws StructureException
```
    run an alignment and also send a bean containing the parameters.
    
    Parameters:
    
    ca1 -
    
    ca2 -
    
    params -
    
    Returns:
    
    the afpChain object that contains the alignment.
    
    Throws:
    
    StructureException
  - getParameters
```
ConfigStrucAligParams getParameters()
```
    Return the paramers for this algorithm.
    
    Returns:
    
    The returned object will be a Java bean.
  - setParameters
```
void setParameters(ConfigStrucAligParams parameters)
```
    Set the default parameters for this algorithm to use
    
    Parameters:
    
    parameters -
  - getAlgorithmName
```
String getAlgorithmName()
```
    Get the name of the Algorithm
    
    Returns:
    
    the name of the algorithm
  - getVersion
```
String getVersion()
```
    Get the Version information for this Algorithm.
    
    Returns:
    
    the version of the algorithm