java.util.concurrent.Callable<MultipleAlignment>
public class MultipleMcOptimizer extends java.lang.Object implements java.util.concurrent.Callable<MultipleAlignment>
The seed alignment can be flexible, non-topological or include CP, but this
optimization will not change the number of flexible parts BlockSet
s
or non-topological regions Block
. Thus, the definition of those parts
depend exclusively on the pairwise alignment (or user alignment) used to
generate the seed multiple alignment.
This class implements Callable, because multiple instances of the optimization can be run in parallel.
Constructor | Description |
---|---|
MultipleMcOptimizer(MultipleAlignment seedAln,
MultipleMcParameters params,
int reference) |
Constructor.
|
Modifier and Type | Method | Description |
---|---|---|
MultipleAlignment |
call() |
|
MultipleAlignment |
optimize() |
Optimization method based in a Monte-Carlo approach.
|
public MultipleMcOptimizer(MultipleAlignment seedAln, MultipleMcParameters params, int reference)
seedAln
- MultipleAlignment to be optimized.params
- the parameter beamreference
- the index of the most similar structure to all othersStructureException
public MultipleAlignment call() throws java.lang.Exception
call
in interface java.util.concurrent.Callable<MultipleAlignment>
java.lang.Exception
public MultipleAlignment optimize() throws StructureException
StructureException