Package org.biojava.nbio.structure.align.multiple.mc

Class MultipleMcMain

java.lang.Object

org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

All Implemented Interfaces:

MultipleStructureAligner

public class MultipleMcMain
extends Object
implements MultipleStructureAligner

Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, as it was originally described by C.Guda, E.D.Scheeff, P.E. Bourne and I.N. Shindyalov (2001). The original CEMC paper is available from here.

This implementation is a generalized version that allows any pairwise structure alignment algorithm as input, thus supporting any non-topological or flexible alignment. The seed can also directly be the input for the optimization. For that, look at MultipleMcOptimizer.

A Demo on how to use the algorithm can be found in the demo package.

Since:

4.1.0

Author:

Aleix Lafita

Field Summary

Fields

Modifier and Type	Field	Description
static final String	algorithmName
static final String	version	Version history:

Constructor Summary

Constructors

Constructor	Description
MultipleMcMain(StructureAlignment pairwiseAlgo)	Default constructor.

Method Summary

Modifier and Type	Method	Description
MultipleAlignment	align(List<Atom[]> atomArrays)	Run an alignment while specifying the atoms to be aligned.
MultipleAlignment	align(List<Atom[]> atomArrays, Object parameters)	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.

Methods inherited from class java.lang.Object

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

Field Details

version

public static final String version

Version history:

1.0 - Initial code implementation from CEMC article.

1.1 - Support CP, non-topological and flexible seed alignments.

See Also:

• Constant Field Values

algorithmName

public static final String algorithmName

See Also:

• Constant Field Values

Constructor Details

MultipleMcMain

public MultipleMcMain(StructureAlignment pairwiseAlgo)

Default constructor. Default parameters are used.

Parameters:

pairwiseAlgo - the pairwise structure alignment used to generate the multiple alignment seed.

Method Details

align

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

Description copied from interface: MultipleStructureAligner

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

Specified by:

align in interface MultipleStructureAligner

Parameters:

atomArrays - List of Atoms of all the structures

Returns:

MultipleAlignment object that contains the alignment.

Throws:

StructureException

See Also:

• MultipleStructureAligner.align(List)

align

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

Description copied from interface: MultipleStructureAligner

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

Specified by:

align in interface MultipleStructureAligner

Parameters:

atomArrays - List of Atoms of all the structures

Returns:

MultipleAlignment object that contains the alignment.

Throws:

StructureException

See Also:

• MultipleStructureAligner.align(List,Object)

getParameters

public ConfigStrucAligParams getParameters()

Description copied from interface: MultipleStructureAligner

Return the parameters of this algorithm instance.

Specified by:

getParameters in interface MultipleStructureAligner

Returns:

The returned Object will be a Java bean.

setParameters

public void setParameters(ConfigStrucAligParams parameters)

Description copied from interface: MultipleStructureAligner

Set the parameters for this algorithm to use.

Specified by:

setParameters in interface MultipleStructureAligner

Parameters:

parameters -

getAlgorithmName

public String getAlgorithmName()

Description copied from interface: MultipleStructureAligner

Get the name of this Algorithm.

Specified by:

getAlgorithmName in interface MultipleStructureAligner

Returns:

String name of the algorithm

getVersion

public String getVersion()

Description copied from interface: MultipleStructureAligner

Get the Version information for this Algorithm.

Specified by:

getVersion in interface MultipleStructureAligner

Returns:

String version of the algorithm