org.biojava.nbio.structure.align.cemc

Class CeMcMain

java.lang.Object

org.biojava.nbio.structure.align.cemc.CeMcMain

All Implemented Interfaces:

MultipleStructureAligner

public class CeMcMain
extends java.lang.Object
implements MultipleStructureAligner

The 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.

The usage follows the MultipleStructureAligner interface. A Demo on how to use the algorithm can be found in DemoCEMC.

Author:

Aleix Lafita

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	algorithmName
static java.lang.String	version Version history:

Constructor Summary

Constructors

Constructor and Description
CeMcMain() Default constructor.

Method Summary

Methods

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

version

public static final java.lang.String version

Version history:

1.0 - Initial code implementation from CEMC article without partial gaps.

2.0 - Update to support CP and partial gaps.

See Also:

Constant Field Values

algorithmName

public static final java.lang.String algorithmName

See Also:

Constant Field Values

Constructor Detail

CeMcMain

public CeMcMain()

Default constructor. Default parameters are used.

Method Detail

align

public MultipleAlignment align(java.util.List<Atom[]> atomArrays,
                      java.lang.Object params)
                        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(java.util.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

getAlgorithmName

public java.lang.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 java.lang.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