Class MultipleMcMain
java.lang.Object
org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
- All Implemented Interfaces:
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionRun an alignment while specifying the atoms to be aligned.Run an alignment and also send a bean containing the parameters.Get the name of this Algorithm.Return the parameters of this algorithm instance.Get the Version information for this Algorithm.voidsetParameters(ConfigStrucAligParams parameters) Set the parameters for this algorithm to use.
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Field Details
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version
Version history:1.0 - Initial code implementation from CEMC article.
1.1 - Support CP, non-topological and flexible seed alignments.
- See Also:
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algorithmName
- See Also:
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Constructor Details
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MultipleMcMain
Default constructor. Default parameters are used.- Parameters:
pairwise- the pairwise structure alignment used to generate the multiple alignment seed.
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Method Details
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align
public MultipleAlignment align(List<Atom[]> atomArrays, Object parameters) throws StructureException Description copied from interface:MultipleStructureAlignerRun an alignment and also send a bean containing the parameters.- Specified by:
alignin interfaceMultipleStructureAligner- Parameters:
atomArrays- List of Atoms of all the structures- Returns:
- MultipleAlignment object that contains the alignment.
- Throws:
StructureException- See Also:
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align
Description copied from interface:MultipleStructureAlignerRun an alignment while specifying the atoms to be aligned. The default parameters for the algorithm are used.- Specified by:
alignin interfaceMultipleStructureAligner- Parameters:
atomArrays- List of Atoms of all the structures- Returns:
- MultipleAlignment object that contains the alignment.
- Throws:
StructureException- See Also:
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getParameters
Description copied from interface:MultipleStructureAlignerReturn the parameters of this algorithm instance.- Specified by:
getParametersin interfaceMultipleStructureAligner- Returns:
- The returned Object will be a Java bean.
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setParameters
Description copied from interface:MultipleStructureAlignerSet the parameters for this algorithm to use.- Specified by:
setParametersin interfaceMultipleStructureAligner
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getAlgorithmName
Description copied from interface:MultipleStructureAlignerGet the name of this Algorithm.- Specified by:
getAlgorithmNamein interfaceMultipleStructureAligner- Returns:
- String name of the algorithm
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getVersion
Description copied from interface:MultipleStructureAlignerGet the Version information for this Algorithm.- Specified by:
getVersionin interfaceMultipleStructureAligner- Returns:
- String version of the algorithm
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