Class StandardDnaFoldingProvider

java.lang.Object

org.episteme.natural.biology.structure.providers.StandardDnaFoldingProvider

All Implemented Interfaces:

AlgorithmProvider, DnaFoldingProvider

public class StandardDnaFoldingProvider
extends Object
implements DnaFoldingProvider

Standard implementation of DNA/RNA folding using a Metropolis-Hastings energy model.

Constructor Summary

Constructors

Constructor	Description
StandardDnaFoldingProvider()

Method Summary

Modifier and Type	Method	Description
double	calculateEnergy(double[][] points, String sequence)
double	calculateEnergy(double[] flat, String sequence)
float	calculateEnergy(float[][] points, String sequence)
float	calculateEnergy(float[] flat, String sequence)
Real	calculateEnergy(List<Real[]> points, String sequence)	Calculates energy for a 3D structure.
String	getAlgorithmType()	Returns the unique category of the algorithm.
String	getName()
void	step(double[][] points, String sequence, double temperature, long seed)
void	step(double[] flat, String sequence, double temperature, long seed)
void	step(float[][] points, String sequence, float temperature, long seed)
void	step(float[] flat, String sequence, float temperature, long seed)
void	step(List<Real[]> points, String sequence, double temperature, long seed)	Performs a single Monte-Carlo step.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface AlgorithmProvider

description, getMetadata, getPriority, isAvailable, score, shutdown

Constructor Details

StandardDnaFoldingProvider

public StandardDnaFoldingProvider()

Method Details

calculateEnergy

public Real calculateEnergy(List<Real[]> points,
 String sequence)

Description copied from interface: DnaFoldingProvider

Calculates energy for a 3D structure.

Specified by:

calculateEnergy in interface DnaFoldingProvider

calculateEnergy

public double calculateEnergy(double[][] points,
 String sequence)

Specified by:

calculateEnergy in interface DnaFoldingProvider

calculateEnergy

public float calculateEnergy(float[][] points,
 String sequence)

Specified by:

calculateEnergy in interface DnaFoldingProvider

step

public void step(List<Real[]> points,
 String sequence,
 double temperature,
 long seed)

Description copied from interface: DnaFoldingProvider

Performs a single Monte-Carlo step.

Specified by:

step in interface DnaFoldingProvider

step

public void step(double[][] points,
 String sequence,
 double temperature,
 long seed)

Specified by:

step in interface DnaFoldingProvider

step

public void step(float[][] points,
 String sequence,
 float temperature,
 long seed)

Specified by:

step in interface DnaFoldingProvider

calculateEnergy

public double calculateEnergy(double[] flat,
 String sequence)

Specified by:

calculateEnergy in interface DnaFoldingProvider

calculateEnergy

public float calculateEnergy(float[] flat,
 String sequence)

Specified by:

calculateEnergy in interface DnaFoldingProvider

step

public void step(double[] flat,
 String sequence,
 double temperature,
 long seed)

Specified by:

step in interface DnaFoldingProvider

step

public void step(float[] flat,
 String sequence,
 float temperature,
 long seed)

Specified by:

step in interface DnaFoldingProvider

getName

public String getName()

Specified by:

getName in interface AlgorithmProvider

getAlgorithmType

public String getAlgorithmType()

Description copied from interface: AlgorithmProvider

Returns the unique category of the algorithm.

Specified by:

getAlgorithmType in interface AlgorithmProvider