R
- The result type of the alignment algorithm.public class ParallelProcessingEngine<R> extends Object
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULTTHREADNUM |
static int |
SHOW_STEPS |
Constructor and Description |
---|
ParallelProcessingEngine(AlignmentAlgorithm<R> algorithm,
Sequence[] sequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
Modifier and Type | Method and Description |
---|---|
void |
calculate()
This starts the calculation of the pairwise alignment of the input
Sequencs according to the given algorithm.
|
AlignmentAlgorithm<R> |
getAlgorithm() |
boolean[][] |
getDoCalculation()
Please refer to the corresponding setter method for more information.
|
int |
getNumberOfThreads()
Please refer to the corresponding setter method for more information.
|
R[][] |
getResultMatrix()
This returns the matrix of results if the calculation is done or null if
it has not finished yet.
|
double[][] |
getScoreMatrix()
This method will only work if the Result class is Double.
|
Sequence[] |
getSequences() |
boolean |
isFinished() |
boolean |
isIgnoreExceptions()
If this is set to true exceptions in single threads are ignored.
|
boolean |
isSymmetric()
Please refer to the corresponding setter method for more information.
|
boolean |
isVerbose()
If verbose is set to true the ParallelProcessingEngine will give
information about the current state of the calculation.
|
void |
setDoCalculation(boolean[][] doCalculation)
This enables a user to specifically set which pairwise similarity
calculations should be done and which should not be done.
|
void |
setIgnoreExceptions(boolean ignoreExceptions)
If this is set to true exceptions in single threads are ignored.
|
void |
setNumberOfThreads(int numThreads)
Sets the number of threads that are used.
|
void |
setSymmetric(boolean symmetric)
If this is set to true it is assumed that the desired result of the
alignment is symmetric, meaning that the alignment between the sequences
i and j is equal to the alignment between j and i.
|
void |
setVerbose(boolean verbose)
If verbose is set to true the ParallelProcessingEngine will give
information about the current state of the calculation.
|
public static final int DEFAULTTHREADNUM
public static final int SHOW_STEPS
public ParallelProcessingEngine(AlignmentAlgorithm<R> algorithm, Sequence[] sequences)
algorithm
- an AlignmentAlgorithm of your choice.sequences
- an array of Sequences. Per default the
ParallelProcessingEngine will calculate all pairwise alignments between
them.public AlignmentAlgorithm<R> getAlgorithm()
public Sequence[] getSequences()
public void setVerbose(boolean verbose)
verbose
- true or false.public boolean isVerbose()
public boolean isIgnoreExceptions()
public void setIgnoreExceptions(boolean ignoreExceptions)
ignoreExceptions
- true if exceptions should be ignored.public void setDoCalculation(boolean[][] doCalculation)
doCalculation
- a S x S - matrix that specifies which pairwise
alignment calculations should be done.public boolean[][] getDoCalculation()
public void setNumberOfThreads(int numThreads)
numThreads
- the number of threads that are used.public int getNumberOfThreads()
public void setSymmetric(boolean symmetric)
symmetric
- true or false.public boolean isSymmetric()
public R[][] getResultMatrix()
public double[][] getScoreMatrix()
public boolean isFinished()
public void calculate()
Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, Georg Zentgraf, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs