MultipleMcMain

java.lang.Object
- org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

All Implemented Interfaces:

MultipleStructureAligner
```
public class MultipleMcMain
extends java.lang.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 java.lang.String algorithmName

static java.lang.String version
Version history:

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

Constructor Summary

Constructors
Constructor Description

MultipleMcMain(StructureAlignment pairwiseAlgo)
Default constructor.

Constructors
Constructor	Description
`MultipleMcMain(StructureAlignment pairwiseAlgo)`	Default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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 parameters)`	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.
    1.1 - Support CP, non-topological and flexible seed alignments.
    
    See Also:
    
    Constant Field Values
  - algorithmName
```
public static final java.lang.String algorithmName
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MultipleMcMain
```
public MultipleMcMain(StructureAlignment pairwiseAlgo)
```
    Default constructor. Default parameters are used.
    
    Parameters:
    
    pairwise - the pairwise structure alignment used to generate the multiple alignment seed.
- Method Detail
  - align
```
public MultipleAlignment align(java.util.List<Atom[]> atomArrays,
                               java.lang.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(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

Class MultipleMcMain

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

version

algorithmName

Constructor Detail

MultipleMcMain

Method Detail

align

align

getParameters

setParameters

getAlgorithmName

getVersion