ur_rna.RNAstructure.backend

Class RNA

java.lang.Object

ur_rna.RNAstructure.backend.Thermodynamics

ur_rna.RNAstructure.backend.RNA

Direct Known Subclasses:

HybridRNA

public class RNA
extends Thermodynamics

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
	RNA()
	RNA(boolean IsRNA)
protected	RNA(long cPtr, boolean cMemoryOwn)
	RNA(java.lang.String sequence)
	RNA(java.lang.String sequence, boolean IsRNA)
	RNA(java.lang.String filename, int fileType)
	RNA(java.lang.String filename, int fileType, boolean IsRNA)
	RNA(java.lang.String filepathOrSequence, int fileType, java.lang.String alphabetName)
	RNA(java.lang.String filepathOrSequence, int fileType, java.lang.String alphabetName, boolean allowUnknownBases)
	RNA(java.lang.String filepathOrSequence, int fileType, java.lang.String alphabetName, boolean allowUnknownBases, boolean skipThermoTables)
	RNA(java.lang.String filepathOrSequence, int fileType, Thermodynamics copyThermo)

Method Summary

Modifier and Type	Method and Description
int	AddComment(java.lang.String comment)
int	AddComment(java.lang.String comment, int structurenumber)
int	BreakPseudoknot()
int	BreakPseudoknot(boolean minimum_energy)
int	BreakPseudoknot(boolean minimum_energy, int structurenumber)
int	BreakPseudoknot(boolean minimum_energy, int structurenumber, boolean useFastMethod)
double	CalculateFreeEnergy()
double	CalculateFreeEnergy(int structurenumber)
double	CalculateFreeEnergy(int structurenumber, boolean UseSimpleMBLoopRules)
boolean	ContainsPseudoknot(int structurenumber)
void	CopyThermo(Thermodynamics copy)
void	delete()
int	DetermineDrawingCoordinates(int height, int width)
int	DetermineDrawingCoordinates(int height, int width, int structurenumber)
void	EnsureStructureCapcacity(int minimumStructures)
protected void	finalize()
int	FoldSingleStrand()
int	FoldSingleStrand(float percent)
int	FoldSingleStrand(float percent, int maximumstructures)
int	FoldSingleStrand(float percent, int maximumstructures, int window)
int	FoldSingleStrand(float percent, int maximumstructures, int window, java.lang.String savefile)
int	FoldSingleStrand(float percent, int maximumstructures, int window, java.lang.String savefile, int maxinternalloopsize)
int	FoldSingleStrand(float percent, int maximumstructures, int window, java.lang.String savefile, int maxinternalloopsize, boolean mfeonly)
int	FoldSingleStrand(float percent, int maximumstructures, int window, java.lang.String savefile, int maxinternalloopsize, boolean mfeonly, boolean simple_iloops)
int	FoldSingleStrand(float percent, int maximumstructures, int window, java.lang.String savefile, int maxinternalloopsize, boolean mfeonly, boolean simple_iloops, boolean disablecoax)
int	ForceDoubleStranded(int i)
int	ForceFMNCleavage(int i)
int	ForceMaximumPairingDistance(int distance)
int	ForceModification(int i)
int	ForcePair(int i, int j)
int	ForceProhibitPair(int i, int j)
int	ForceSingleStranded(int i)
int	GenerateAllSuboptimalStructures()
int	GenerateAllSuboptimalStructures(float percent)
int	GenerateAllSuboptimalStructures(float percent, double deltaG)
boolean	GetBackboneType()
java.lang.String	GetCommentString()
java.lang.String	GetCommentString(int structurenumber)
protected static long	getCPtr(RNA obj)
double	GetEnsembleDefect()
double	GetEnsembleDefect(int structurenumber)
double	GetEnsembleEnergy()
int	GetErrorCode()
java.lang.String	GetErrorDetails()
static java.lang.String	GetErrorMessage(int error)
int	GetForcedDoubleStranded(int constraintnumber)
int	GetForcedFMNCleavage(int constraintnumber)
int	GetForcedModification(int constraintnumber)
int	GetForcedPair(int constraintnumber, boolean fiveprime)
int	GetForcedProhibitedPair(int constraintnumber, boolean fiveprime)
int	GetForcedSingleStranded(int constraintnumber)
double	GetFreeEnergy(int structurenumber)
java.lang.String	GetFullErrorMessage()
int	getIntAt(int i)
int	getInts(int[] arr, int size)
int	GetLabelXCoordinate(int i)
int	GetLabelYCoordinate(int i)
int	GetMaximumPairingDistance()
char	GetNucleotide(int i)
int	GetNucleotideXCoordinate(int i)
int	GetNucleotideYCoordinate(int i)
int	GetNumberOfForcedDoubleStranded()
int	GetNumberOfForcedFMNCleavages()
int	GetNumberOfForcedModifications()
int	GetNumberOfForcedPairs()
int	GetNumberOfForcedProhibitedPairs()
int	GetNumberOfForcedSingleStranded()
int	GetPair(int i)
int	GetPair(int i, int structurenumber)
double	GetPairEnergy(int i, int j)
int	GetPairProbabilities(double[] arr, int size)
double	GetPairProbability(int i, int j)
ProgressHandler	GetProgress()
java.lang.String	GetSequence()
int	GetSequenceLength()
structure	GetStructure()
int	GetStructureNumber()
void	initInts()
int	MaximizeExpectedAccuracy()
int	MaximizeExpectedAccuracy(double maxPercent)
int	MaximizeExpectedAccuracy(double maxPercent, int maxStructures)
int	MaximizeExpectedAccuracy(double maxPercent, int maxStructures, int window)
int	MaximizeExpectedAccuracy(double maxPercent, int maxStructures, int window, double gamma)
int	PartitionFunction()
int	PartitionFunction(java.lang.String savefile)
int	PartitionFunction(java.lang.String savefile, double temperature)
int	PartitionFunction(java.lang.String savefile, double temperature, boolean disablecoax)
int	PartitionFunction(java.lang.String savefile, double temperature, boolean disablecoax, boolean restoreSHAPE)
int	PredictProbablePairs()
int	PredictProbablePairs(float probability)
int	ProbKnot()
int	ProbKnot(int iterations)
int	ProbKnot(int iterations, int MinHelixLength)
int	ProbKnotFromSample()
int	ProbKnotFromSample(int iterations)
int	ProbKnotFromSample(int iterations, int MinHelixLength)
int	ReadConstraints(java.lang.String filename)
int	ReadDMS(java.lang.String filename)
int	ReadDSO(java.lang.String filename)
int	ReadExperimentalPairBonus(java.lang.String filename, double experimentalOffset, double experimentalScaling)
int	ReadSHAPE(java.lang.String filename, double slope, double intercept)
int	ReadSHAPE(java.lang.String filename, double dsSlope, double dsIntercept, double ssSlope, double ssIntercept)
int	ReadSHAPE(java.lang.String filename, double dsSlope, double dsIntercept, double ssSlope, double ssIntercept, RestraintType modifier)
int	ReadSHAPE(java.lang.String filename, double slope, double intercept, RestraintType modifier)
int	ReadSHAPE(java.lang.String filename, double slope, double intercept, RestraintType modifier, boolean IsPseudoEnergy)
int	ReadSSO(java.lang.String filename)
int	ReFoldSingleStrand()
int	ReFoldSingleStrand(float percent)
int	ReFoldSingleStrand(float percent, int maximumstructures)
int	ReFoldSingleStrand(float percent, int maximumstructures, int window)
int	RemoveBasePair(int i)
int	RemoveBasePair(int i, int structurenumber)
void	RemoveConstraints()
int	RemovePairs()
int	RemovePairs(int structurenumber)
int	RemovePairs(int structurenumber, boolean removeIfLastStructure)
void	ResetError()
void	SetErrorDetails(java.lang.String details)
int	SetExtrinsic(int i, int j, double k)
void	SetProgress(ProgressHandler Progress)
int	SpecifyPair(int i, int j)
int	SpecifyPair(int i, int j, int structurenumber)
int	Stochastic()
int	Stochastic(int structures)
int	Stochastic(int structures, int seed)
void	StopProgress()
int	WriteConstraints(java.lang.String filename)
int	WriteCt(java.lang.String filename)
int	WriteDotBracket(java.lang.String filename)
int	WriteDotBracket(java.lang.String filename, int structurenumber)
int	WriteDotBracket(java.lang.String filename, int structurenumber, DotBracketFormat format)
int	WriteThermodynamicDetails(java.lang.String filename)
int	WriteThermodynamicDetails(java.lang.String filename, boolean UseSimpleMBLoopRules)

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

RNA

public RNA()

RNA

public RNA(boolean IsRNA)

RNA

protected RNA(long cPtr,
              boolean cMemoryOwn)

RNA

public RNA(java.lang.String sequence)

RNA

public RNA(java.lang.String sequence,
           boolean IsRNA)

RNA

public RNA(java.lang.String filename,
           int fileType)

RNA

public RNA(java.lang.String filename,
           int fileType,
           boolean IsRNA)

RNA

public RNA(java.lang.String filepathOrSequence,
           int fileType,
           java.lang.String alphabetName)

RNA

public RNA(java.lang.String filepathOrSequence,
           int fileType,
           java.lang.String alphabetName,
           boolean allowUnknownBases)

RNA

public RNA(java.lang.String filepathOrSequence,
           int fileType,
           java.lang.String alphabetName,
           boolean allowUnknownBases,
           boolean skipThermoTables)

RNA

public RNA(java.lang.String filepathOrSequence,
           int fileType,
           Thermodynamics copyThermo)

Method Detail

AddComment

public int AddComment(java.lang.String comment)

AddComment

public int AddComment(java.lang.String comment,
                      int structurenumber)

BreakPseudoknot

public int BreakPseudoknot()

BreakPseudoknot

public int BreakPseudoknot(boolean minimum_energy)

BreakPseudoknot

public int BreakPseudoknot(boolean minimum_energy,
                           int structurenumber)

BreakPseudoknot

public int BreakPseudoknot(boolean minimum_energy,
                           int structurenumber,
                           boolean useFastMethod)

CalculateFreeEnergy

public double CalculateFreeEnergy()

CalculateFreeEnergy

public double CalculateFreeEnergy(int structurenumber)

CalculateFreeEnergy

public double CalculateFreeEnergy(int structurenumber,
                                  boolean UseSimpleMBLoopRules)

ContainsPseudoknot

public boolean ContainsPseudoknot(int structurenumber)

CopyThermo

public void CopyThermo(Thermodynamics copy)

delete

public void delete()

Overrides:

delete in class Thermodynamics

DetermineDrawingCoordinates

public int DetermineDrawingCoordinates(int height,
                                       int width)

DetermineDrawingCoordinates

public int DetermineDrawingCoordinates(int height,
                                       int width,
                                       int structurenumber)

EnsureStructureCapcacity

public void EnsureStructureCapcacity(int minimumStructures)

finalize

protected void finalize()

Overrides:

finalize in class Thermodynamics

FoldSingleStrand

public int FoldSingleStrand()

FoldSingleStrand

public int FoldSingleStrand(float percent)

FoldSingleStrand

public int FoldSingleStrand(float percent,
                            int maximumstructures)

FoldSingleStrand

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

FoldSingleStrand

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

FoldSingleStrand

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

FoldSingleStrand

public int FoldSingleStrand(float percent,
                            int maximumstructures,
                            int window,
                            java.lang.String savefile,
                            int maxinternalloopsize,
                            boolean mfeonly)

FoldSingleStrand

public int FoldSingleStrand(float percent,
                            int maximumstructures,
                            int window,
                            java.lang.String savefile,
                            int maxinternalloopsize,
                            boolean mfeonly,
                            boolean simple_iloops)

FoldSingleStrand

public int FoldSingleStrand(float percent,
                            int maximumstructures,
                            int window,
                            java.lang.String savefile,
                            int maxinternalloopsize,
                            boolean mfeonly,
                            boolean simple_iloops,
                            boolean disablecoax)

ForceDoubleStranded

public int ForceDoubleStranded(int i)

ForceFMNCleavage

public int ForceFMNCleavage(int i)

ForceMaximumPairingDistance

public int ForceMaximumPairingDistance(int distance)

ForceModification

public int ForceModification(int i)

ForcePair

public int ForcePair(int i,
                     int j)

ForceProhibitPair

public int ForceProhibitPair(int i,
                             int j)

ForceSingleStranded

public int ForceSingleStranded(int i)

GenerateAllSuboptimalStructures

public int GenerateAllSuboptimalStructures()

GenerateAllSuboptimalStructures

public int GenerateAllSuboptimalStructures(float percent)

GenerateAllSuboptimalStructures

public int GenerateAllSuboptimalStructures(float percent,
                                           double deltaG)

GetBackboneType

public boolean GetBackboneType()

GetCommentString

public java.lang.String GetCommentString()

GetCommentString

public java.lang.String GetCommentString(int structurenumber)

getCPtr

protected static long getCPtr(RNA obj)

GetEnsembleDefect

public double GetEnsembleDefect()

GetEnsembleDefect

public double GetEnsembleDefect(int structurenumber)

GetEnsembleEnergy

public double GetEnsembleEnergy()

GetErrorCode

public int GetErrorCode()

GetErrorDetails

public java.lang.String GetErrorDetails()

GetErrorMessage

public static java.lang.String GetErrorMessage(int error)

GetForcedDoubleStranded

public int GetForcedDoubleStranded(int constraintnumber)

GetForcedFMNCleavage

public int GetForcedFMNCleavage(int constraintnumber)

GetForcedModification

public int GetForcedModification(int constraintnumber)

GetForcedPair

public int GetForcedPair(int constraintnumber,
                         boolean fiveprime)

GetForcedProhibitedPair

public int GetForcedProhibitedPair(int constraintnumber,
                                   boolean fiveprime)

GetForcedSingleStranded

public int GetForcedSingleStranded(int constraintnumber)

GetFreeEnergy

public double GetFreeEnergy(int structurenumber)

GetFullErrorMessage

public java.lang.String GetFullErrorMessage()

getIntAt

public int getIntAt(int i)

getInts

public int getInts(int[] arr,
                   int size)

GetLabelXCoordinate

public int GetLabelXCoordinate(int i)

GetLabelYCoordinate

public int GetLabelYCoordinate(int i)

GetMaximumPairingDistance

public int GetMaximumPairingDistance()

GetNucleotide

public char GetNucleotide(int i)

GetNucleotideXCoordinate

public int GetNucleotideXCoordinate(int i)

GetNucleotideYCoordinate

public int GetNucleotideYCoordinate(int i)

GetNumberOfForcedDoubleStranded

public int GetNumberOfForcedDoubleStranded()

GetNumberOfForcedFMNCleavages

public int GetNumberOfForcedFMNCleavages()

GetNumberOfForcedModifications

public int GetNumberOfForcedModifications()

GetNumberOfForcedPairs

public int GetNumberOfForcedPairs()

GetNumberOfForcedProhibitedPairs

public int GetNumberOfForcedProhibitedPairs()

GetNumberOfForcedSingleStranded

public int GetNumberOfForcedSingleStranded()

GetPair

public int GetPair(int i)

GetPair

public int GetPair(int i,
                   int structurenumber)

GetPairEnergy

public double GetPairEnergy(int i,
                            int j)

GetPairProbabilities

public int GetPairProbabilities(double[] arr,
                                int size)

GetPairProbability

public double GetPairProbability(int i,
                                 int j)

GetProgress

public ProgressHandler GetProgress()

GetSequence

public java.lang.String GetSequence()

GetSequenceLength

public int GetSequenceLength()

GetStructure

public structure GetStructure()

GetStructureNumber

public int GetStructureNumber()

initInts

public void initInts()

MaximizeExpectedAccuracy

public int MaximizeExpectedAccuracy()

MaximizeExpectedAccuracy

public int MaximizeExpectedAccuracy(double maxPercent)

MaximizeExpectedAccuracy

public int MaximizeExpectedAccuracy(double maxPercent,
                                    int maxStructures)

MaximizeExpectedAccuracy

public int MaximizeExpectedAccuracy(double maxPercent,
                                    int maxStructures,
                                    int window)

MaximizeExpectedAccuracy

public int MaximizeExpectedAccuracy(double maxPercent,
                                    int maxStructures,
                                    int window,
                                    double gamma)

PartitionFunction

public int PartitionFunction()

PartitionFunction

public int PartitionFunction(java.lang.String savefile)

PartitionFunction

public int PartitionFunction(java.lang.String savefile,
                             double temperature)

PartitionFunction

public int PartitionFunction(java.lang.String savefile,
                             double temperature,
                             boolean disablecoax)

PartitionFunction

public int PartitionFunction(java.lang.String savefile,
                             double temperature,
                             boolean disablecoax,
                             boolean restoreSHAPE)

PredictProbablePairs

public int PredictProbablePairs()

PredictProbablePairs

public int PredictProbablePairs(float probability)

ProbKnot

public int ProbKnot()

ProbKnot

public int ProbKnot(int iterations)

ProbKnot

public int ProbKnot(int iterations,
                    int MinHelixLength)

ProbKnotFromSample

public int ProbKnotFromSample()

ProbKnotFromSample

public int ProbKnotFromSample(int iterations)

ProbKnotFromSample

public int ProbKnotFromSample(int iterations,
                              int MinHelixLength)

ReadConstraints

public int ReadConstraints(java.lang.String filename)

ReadDMS

public int ReadDMS(java.lang.String filename)

ReadDSO

public int ReadDSO(java.lang.String filename)

ReadExperimentalPairBonus

public int ReadExperimentalPairBonus(java.lang.String filename,
                                     double experimentalOffset,
                                     double experimentalScaling)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     double slope,
                     double intercept)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     double dsSlope,
                     double dsIntercept,
                     double ssSlope,
                     double ssIntercept)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     double dsSlope,
                     double dsIntercept,
                     double ssSlope,
                     double ssIntercept,
                     RestraintType modifier)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     double slope,
                     double intercept,
                     RestraintType modifier)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     double slope,
                     double intercept,
                     RestraintType modifier,
                     boolean IsPseudoEnergy)

ReadSSO

public int ReadSSO(java.lang.String filename)

ReFoldSingleStrand

public int ReFoldSingleStrand()

ReFoldSingleStrand

public int ReFoldSingleStrand(float percent)

ReFoldSingleStrand

public int ReFoldSingleStrand(float percent,
                              int maximumstructures)

ReFoldSingleStrand

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

RemoveBasePair

public int RemoveBasePair(int i)

RemoveBasePair

public int RemoveBasePair(int i,
                          int structurenumber)

RemoveConstraints

public void RemoveConstraints()

RemovePairs

public int RemovePairs()

RemovePairs

public int RemovePairs(int structurenumber)

RemovePairs

public int RemovePairs(int structurenumber,
                       boolean removeIfLastStructure)

ResetError

public void ResetError()

SetErrorDetails

public void SetErrorDetails(java.lang.String details)

SetExtrinsic

public int SetExtrinsic(int i,
                        int j,
                        double k)

SetProgress

public void SetProgress(ProgressHandler Progress)

SpecifyPair

public int SpecifyPair(int i,
                       int j)

SpecifyPair

public int SpecifyPair(int i,
                       int j,
                       int structurenumber)

Stochastic

public int Stochastic()

Stochastic

public int Stochastic(int structures)

Stochastic

public int Stochastic(int structures,
                      int seed)

StopProgress

public void StopProgress()

WriteConstraints

public int WriteConstraints(java.lang.String filename)

WriteCt

public int WriteCt(java.lang.String filename)

WriteDotBracket

public int WriteDotBracket(java.lang.String filename)

WriteDotBracket

public int WriteDotBracket(java.lang.String filename,
                           int structurenumber)

WriteDotBracket

public int WriteDotBracket(java.lang.String filename,
                           int structurenumber,
                           DotBracketFormat format)

WriteThermodynamicDetails

public int WriteThermodynamicDetails(java.lang.String filename)

WriteThermodynamicDetails

public int WriteThermodynamicDetails(java.lang.String filename,
                                     boolean UseSimpleMBLoopRules)