ur_rna.RNAstructure.backend

Class HybridRNA

java.lang.Object

ur_rna.RNAstructure.backend.Thermodynamics

ur_rna.RNAstructure.backend.RNA

ur_rna.RNAstructure.backend.HybridRNA

public class HybridRNA
extends RNA

Field Summary

Fields

Modifier and Type	Field and Description
private long	swigCPtr

Fields inherited from class ur_rna.RNAstructure.backend.Thermodynamics

swigCMemOwn

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	HybridRNA(long cPtr, boolean cMemoryOwn)
	HybridRNA(java.lang.String filename1, int type1, java.lang.String filename2, int type2)
	HybridRNA(java.lang.String filename1, int type1, java.lang.String filename2, int type2, boolean IsRNA)
	HybridRNA(java.lang.String filename1, int type1, java.lang.String filename2, int type2, java.lang.String alphabet)
	HybridRNA(java.lang.String sequence1, java.lang.String sequence2)
	HybridRNA(java.lang.String sequence1, java.lang.String sequence2, boolean IsRNA)

Method Summary

Modifier and Type	Method and Description
int	AccessFold()
int	AccessFold(double gamma)
int	AccessFold(double gamma, float percent)
int	AccessFold(double gamma, float percent, int maximumstructures)
int	AccessFold(double gamma, float percent, int maximumstructures, int window)
int	AccessFold(double gamma, float percent, int maximumstructures, int window, int maxinternalloopsize)
void	delete()
protected void	finalize()
int	FoldBimolecular()
int	FoldBimolecular(float percent)
int	FoldBimolecular(float percent, int maximumstructures)
int	FoldBimolecular(float percent, int maximumstructures, int window)
int	FoldBimolecular(float percent, int maximumstructures, int window, java.lang.String savefile)
int	FoldBimolecular(float percent, int maximumstructures, int window, java.lang.String savefile, int maxinternalloopsize)
int	FoldDuplex()
int	FoldDuplex(float percent)
int	FoldDuplex(float percent, int maximumstructures)
int	FoldDuplex(float percent, int maximumstructures, int window)
int	FoldDuplex(float percent, int maximumstructures, int window, int maxinternalloopsize)
protected static long	getCPtr(HybridRNA obj)
int	GetErrorCode()
boolean	GetForbidIntramolecular()
java.lang.String	GetMyErrorMessage(int error)
RNA	GetRNA1()
RNA	GetRNA2()
int	PartitionFunctionBimolecular()
int	PartitionFunctionBimolecular(java.lang.String savefile)
void	SetForbidIntramolecular(boolean forbid)
void	SetProgress(ProgressHandler Progress)
void	StopProgress()

Methods inherited from class ur_rna.RNAstructure.backend.RNA

AddComment, AddComment, BreakPseudoknot, BreakPseudoknot, BreakPseudoknot, BreakPseudoknot, CalculateFreeEnergy, CalculateFreeEnergy, CalculateFreeEnergy, ContainsPseudoknot, CopyThermo, DetermineDrawingCoordinates, DetermineDrawingCoordinates, EnsureStructureCapcacity, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, FoldSingleStrand, ForceDoubleStranded, ForceFMNCleavage, ForceMaximumPairingDistance, ForceModification, ForcePair, ForceProhibitPair, ForceSingleStranded, GenerateAllSuboptimalStructures, GenerateAllSuboptimalStructures, GenerateAllSuboptimalStructures, GetBackboneType, GetCommentString, GetCommentString, getCPtr, GetEnsembleDefect, GetEnsembleDefect, GetEnsembleEnergy, GetErrorDetails, GetErrorMessage, GetForcedDoubleStranded, GetForcedFMNCleavage, GetForcedModification, GetForcedPair, GetForcedProhibitedPair, GetForcedSingleStranded, GetFreeEnergy, GetFullErrorMessage, getIntAt, getInts, GetLabelXCoordinate, GetLabelYCoordinate, GetMaximumPairingDistance, GetNucleotide, GetNucleotideXCoordinate, GetNucleotideYCoordinate, GetNumberOfForcedDoubleStranded, GetNumberOfForcedFMNCleavages, GetNumberOfForcedModifications, GetNumberOfForcedPairs, GetNumberOfForcedProhibitedPairs, GetNumberOfForcedSingleStranded, GetPair, GetPair, GetPairEnergy, GetPairProbabilities, GetPairProbability, GetProgress, GetSequence, GetSequenceLength, GetStructure, GetStructureNumber, initInts, MaximizeExpectedAccuracy, MaximizeExpectedAccuracy, MaximizeExpectedAccuracy, MaximizeExpectedAccuracy, MaximizeExpectedAccuracy, PartitionFunction, PartitionFunction, PartitionFunction, PartitionFunction, PartitionFunction, PredictProbablePairs, PredictProbablePairs, ProbKnot, ProbKnot, ProbKnot, ProbKnotFromSample, ProbKnotFromSample, ProbKnotFromSample, ReadConstraints, ReadDMS, ReadDSO, ReadExperimentalPairBonus, ReadSHAPE, ReadSHAPE, ReadSHAPE, ReadSHAPE, ReadSHAPE, ReadSSO, ReFoldSingleStrand, ReFoldSingleStrand, ReFoldSingleStrand, ReFoldSingleStrand, RemoveBasePair, RemoveBasePair, RemoveConstraints, RemovePairs, RemovePairs, RemovePairs, ResetError, SetErrorDetails, SetExtrinsic, SpecifyPair, SpecifyPair, Stochastic, Stochastic, Stochastic, WriteConstraints, WriteCt, WriteDotBracket, WriteDotBracket, WriteDotBracket, WriteThermodynamicDetails, WriteThermodynamicDetails

Methods inherited from class ur_rna.RNAstructure.backend.Thermodynamics

ClearEnergies, ClearEnthalpies, GetAlphabetName, getCPtr, GetDatatable, GetEnergyRead, GetEnthalpyTable, GetEnthalpyTable, getIsrna, GetTemperature, IsAlphabetRead, ReadThermodynamic, ReadThermodynamic, ReadThermodynamic, ReadThermodynamic, ReloadDataTables, ReloadDataTables, setIsrna, SetTemperature, VerifyThermodynamic

Methods inherited from class java.lang.Object

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

Field Detail

swigCPtr

private transient long swigCPtr

Constructor Detail

HybridRNA

protected HybridRNA(long cPtr,
                    boolean cMemoryOwn)

HybridRNA

public HybridRNA(java.lang.String filename1,
                 int type1,
                 java.lang.String filename2,
                 int type2)

HybridRNA

public HybridRNA(java.lang.String filename1,
                 int type1,
                 java.lang.String filename2,
                 int type2,
                 boolean IsRNA)

HybridRNA

public HybridRNA(java.lang.String filename1,
                 int type1,
                 java.lang.String filename2,
                 int type2,
                 java.lang.String alphabet)

HybridRNA

public HybridRNA(java.lang.String sequence1,
                 java.lang.String sequence2)

HybridRNA

public HybridRNA(java.lang.String sequence1,
                 java.lang.String sequence2,
                 boolean IsRNA)

Method Detail

AccessFold

public int AccessFold()

AccessFold

public int AccessFold(double gamma)

AccessFold

public int AccessFold(double gamma,
                      float percent)

AccessFold

public int AccessFold(double gamma,
                      float percent,
                      int maximumstructures)

AccessFold

public int AccessFold(double gamma,
                      float percent,
                      int maximumstructures,
                      int window)

AccessFold

public int AccessFold(double gamma,
                      float percent,
                      int maximumstructures,
                      int window,
                      int maxinternalloopsize)

delete

public void delete()

Overrides:

delete in class RNA

finalize

protected void finalize()

Overrides:

finalize in class RNA

FoldBimolecular

public int FoldBimolecular()

FoldBimolecular

public int FoldBimolecular(float percent)

FoldBimolecular

public int FoldBimolecular(float percent,
                           int maximumstructures)

FoldBimolecular

public int FoldBimolecular(float percent,
                           int maximumstructures,
                           int window)

FoldBimolecular

public int FoldBimolecular(float percent,
                           int maximumstructures,
                           int window,
                           java.lang.String savefile)

FoldBimolecular

public int FoldBimolecular(float percent,
                           int maximumstructures,
                           int window,
                           java.lang.String savefile,
                           int maxinternalloopsize)

FoldDuplex

public int FoldDuplex()

FoldDuplex

public int FoldDuplex(float percent)

FoldDuplex

public int FoldDuplex(float percent,
                      int maximumstructures)

FoldDuplex

public int FoldDuplex(float percent,
                      int maximumstructures,
                      int window)

FoldDuplex

public int FoldDuplex(float percent,
                      int maximumstructures,
                      int window,
                      int maxinternalloopsize)

getCPtr

protected static long getCPtr(HybridRNA obj)

GetErrorCode

public int GetErrorCode()

Overrides:

GetErrorCode in class RNA

GetForbidIntramolecular

public boolean GetForbidIntramolecular()

GetMyErrorMessage

public java.lang.String GetMyErrorMessage(int error)

GetRNA1

public RNA GetRNA1()

GetRNA2

public RNA GetRNA2()

PartitionFunctionBimolecular

public int PartitionFunctionBimolecular()

PartitionFunctionBimolecular

public int PartitionFunctionBimolecular(java.lang.String savefile)

SetForbidIntramolecular

public void SetForbidIntramolecular(boolean forbid)

SetProgress

public void SetProgress(ProgressHandler Progress)

Overrides:

SetProgress in class RNA

StopProgress

public void StopProgress()

Overrides:

StopProgress in class RNA