org.biojava.nbio.structure.align

Interface MultipleStructureAligner

All Known Implementing Classes:

MultipleMcMain

public interface MultipleStructureAligner

Interface for the Multiple Structure Alignment Algorithms. The Pairwise Alignment Algorithms can also implement this class to be able to return MultipleAlignment Objects.

Author:

Aleix Lafita

Method Summary

Modifier and Type	Method and Description
MultipleAlignment	align(List<Atom[]> atomArrays) Run an alignment while specifying the atoms to be aligned.
MultipleAlignment	align(List<Atom[]> atomArrays, Object params) Run an alignment and also send a bean containing the parameters.
String	getAlgorithmName() Get the name of this Algorithm.
ConfigStrucAligParams	getParameters() Return the parameters of this algorithm instance.
String	getVersion() Get the Version information for this Algorithm.
void	setParameters(ConfigStrucAligParams parameters) Set the parameters for this algorithm to use.

Method Detail

align

MultipleAlignment align(List<Atom[]> atomArrays)
                 throws StructureException

Run an alignment while specifying the atoms to be aligned. The default parameters for the algorithm are used.

Parameters:

atomArrays - List of Atoms of all the structures

Returns:

MultipleAlignment object that contains the alignment.

Throws:

StructureException

See Also:

align(List,Object)

align

MultipleAlignment align(List<Atom[]> atomArrays,
                        Object params)
                 throws StructureException

Run an alignment and also send a bean containing the parameters.

Parameters:

atomArrays - List of Atoms of all the structures

Returns:

MultipleAlignment object that contains the alignment.

Throws:

StructureException

See Also:

align(List)

getParameters

ConfigStrucAligParams getParameters()

Return the parameters of this algorithm instance.

Returns:

The returned Object will be a Java bean.

setParameters

void setParameters(ConfigStrucAligParams parameters)

Set the parameters for this algorithm to use.

Parameters:

parameters -

getAlgorithmName

String getAlgorithmName()

Get the name of this Algorithm.

Returns:

String name of the algorithm

getVersion

String getVersion()

Get the Version information for this Algorithm.

Returns:

String version of the algorithm