ur_rna.RNAstructure.backend

Class structure

java.lang.Object

ur_rna.RNAstructure.backend.structure

public class structure
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	swigCMemOwn
private long	swigCPtr

Constructor Summary

Constructors

Modifier	Constructor and Description
	structure()
	structure(int structures)
protected	structure(long cPtr, boolean cMemoryOwn)

Method Summary

Modifier and Type	Method and Description
void	AddDouble(int i)
void	AddForbiddenPair(int i, int j)
void	AddGUPair(int i)
void	AddModified(int i)
void	AddPair(int i, int j)
void	AddSingle(int i)
void	AddStructure()
void	allocateconstant()
void	AllocateSHAPE()
void	allocatetem()
void	BreakPseudoknots(int structurenumber)
void	CleanStructure(int structurenumber)
int	ctout(java.lang.String ctoutfile)
void	delete()
void	DeleteSHAPE()
boolean	DistanceLimited()
protected void	finalize()
void	FindPseudoknots(int structurenumber)
void	FindPseudoknots(int structurenumber, CIntVector pseudoknotPairs)
void	FindPseudoknots(int structurenumber, CIntVector pseudoknotPairs, CIntVector normalPairs)
int	GetBase(int i)
protected static long	getCPtr(structure obj)
java.lang.String	GetCtLabel(int structurenumber)
int	GetDouble(int i)
int	GetEnergy(int structurenumber)
java.lang.String	GetErrorDetails()
int	GetForbiddenPair3(int i)
int	GetForbiddenPair5(int i)
int	GetGUpair(int i)
static double	getKT()
int	GetModified(int i)
int	GetNumberofDoubles()
int	GetNumberofForbiddenPairs()
int	GetNumberofGU()
int	GetNumberofModified()
int	GetNumberofPairs()
int	GetNumberofSingles()
int	GetNumberofStructures()
int	GetPair(int i)
int	GetPair(int i, int structurenumber)
int	GetPair3(int i)
int	GetPair5(int i)
int	GetPairingDistanceLimit()
void	GetPseudoknotRanks(CIntVector results)
void	GetPseudoknotRanks(CIntVector results, int structurenumber)
java.lang.String	GetSequence()
java.lang.String	GetSequenceLabel()
int	GetSequenceLength()
boolean	getSHAPEFileRead()
static int	getShowWarnings()
int	GetSingle(int i)
static boolean	getSumShapeRepeats()
datatable	GetThermodynamicDataTable()
boolean	HasPseudoknots()
boolean	HasPseudoknots(int structurenumber)
boolean	IsAlphabetLoaded()
boolean	IsNuc(int i, char c)
boolean	IsNuc(int i, char c, datatable data)
boolean	IsThermoDataLoaded()
int	openct(java.lang.String ctfile)
int	opendbn(java.lang.String bracketFile)
int	openseq(java.lang.String seqfile)
int	openseqx(java.lang.String seqfile)
boolean	ProblemwithStructures()
int	ReadExperimentalPairBonus(java.lang.String filename)
int	ReadExperimentalPairBonus(java.lang.String filename, double experimentalOffset)
int	ReadExperimentalPairBonus(java.lang.String filename, double experimentalOffset, double experimentalScaling)
int	ReadOffset(java.lang.String SSOffset, java.lang.String DSOffset)
int	ReadSHAPE(java.lang.String filename)
int	ReadSHAPE(java.lang.String filename, float SingleStrandThreshold, float ModificationThreshold)
int	ReadSHAPE(java.lang.String filename, RestraintType modifier)
int	ReadSHAPE(java.lang.String filename, RestraintType modifier, boolean calculatePseudoEnergies)
void	RemoveAllStructures()
void	RemoveConstraints()
void	RemoveEnergyLabels()
void	RemoveEnergyLabels(java.lang.String customLabel)
void	RemoveLastStructure()
void	RemovePair(int i)
void	RemovePair(int i, int structurenumber)
void	RemoveStructure(int structurenumber)
void	SetCtLabel(java.lang.String label, int structurenumber)
void	SetEnergy(int structurenumber, int energy)
void	SetPair(int i, int j)
void	SetPair(int i, int j, int structurenumber)
void	SetPairingDistance(int maxdistance)
int	SetSequence(java.lang.String sequence)
void	SetSequenceLabel(java.lang.String label)
void	setSHAPEFileRead(boolean value)
static void	setShowWarnings(int value)
static void	setSumShapeRepeats(boolean value)
void	SetThermodynamicDataTable(datatable DataTablePointer)
void	sort()
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	writeseq(java.lang.String seqfile)
int	writeseq(java.lang.String seqfile, int seqFileType)
int	writeseq(java.lang.String seqfile, int seqFileType, boolean append)
int	WriteSHAPE(java.lang.String outfile)
int	WriteSHAPE(java.lang.String outfile, boolean printHeaders)

Methods inherited from class java.lang.Object

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

Field Detail

swigCMemOwn

protected transient boolean swigCMemOwn

swigCPtr

private transient long swigCPtr

Constructor Detail

structure

public structure()

structure

public structure(int structures)

structure

protected structure(long cPtr,
                    boolean cMemoryOwn)

Method Detail

AddDouble

public void AddDouble(int i)

AddForbiddenPair

public void AddForbiddenPair(int i,
                             int j)

AddGUPair

public void AddGUPair(int i)

AddModified

public void AddModified(int i)

AddPair

public void AddPair(int i,
                    int j)

AddSingle

public void AddSingle(int i)

AddStructure

public void AddStructure()

allocateconstant

public void allocateconstant()

AllocateSHAPE

public void AllocateSHAPE()

allocatetem

public void allocatetem()

BreakPseudoknots

public void BreakPseudoknots(int structurenumber)

CleanStructure

public void CleanStructure(int structurenumber)

ctout

public int ctout(java.lang.String ctoutfile)

delete

public void delete()

DeleteSHAPE

public void DeleteSHAPE()

DistanceLimited

public boolean DistanceLimited()

finalize

protected void finalize()

Overrides:

finalize in class java.lang.Object

FindPseudoknots

public void FindPseudoknots(int structurenumber)

FindPseudoknots

public void FindPseudoknots(int structurenumber,
                            CIntVector pseudoknotPairs)

FindPseudoknots

public void FindPseudoknots(int structurenumber,
                            CIntVector pseudoknotPairs,
                            CIntVector normalPairs)

GetBase

public int GetBase(int i)

getCPtr

protected static long getCPtr(structure obj)

GetCtLabel

public java.lang.String GetCtLabel(int structurenumber)

GetDouble

public int GetDouble(int i)

GetEnergy

public int GetEnergy(int structurenumber)

GetErrorDetails

public java.lang.String GetErrorDetails()

GetForbiddenPair3

public int GetForbiddenPair3(int i)

GetForbiddenPair5

public int GetForbiddenPair5(int i)

GetGUpair

public int GetGUpair(int i)

getKT

public static double getKT()

GetModified

public int GetModified(int i)

GetNumberofDoubles

public int GetNumberofDoubles()

GetNumberofForbiddenPairs

public int GetNumberofForbiddenPairs()

GetNumberofGU

public int GetNumberofGU()

GetNumberofModified

public int GetNumberofModified()

GetNumberofPairs

public int GetNumberofPairs()

GetNumberofSingles

public int GetNumberofSingles()

GetNumberofStructures

public int GetNumberofStructures()

GetPair

public int GetPair(int i)

GetPair

public int GetPair(int i,
                   int structurenumber)

GetPair3

public int GetPair3(int i)

GetPair5

public int GetPair5(int i)

GetPairingDistanceLimit

public int GetPairingDistanceLimit()

GetPseudoknotRanks

public void GetPseudoknotRanks(CIntVector results)

GetPseudoknotRanks

public void GetPseudoknotRanks(CIntVector results,
                               int structurenumber)

GetSequence

public java.lang.String GetSequence()

GetSequenceLabel

public java.lang.String GetSequenceLabel()

GetSequenceLength

public int GetSequenceLength()

getSHAPEFileRead

public boolean getSHAPEFileRead()

getShowWarnings

public static int getShowWarnings()

GetSingle

public int GetSingle(int i)

getSumShapeRepeats

public static boolean getSumShapeRepeats()

GetThermodynamicDataTable

public datatable GetThermodynamicDataTable()

HasPseudoknots

public boolean HasPseudoknots()

HasPseudoknots

public boolean HasPseudoknots(int structurenumber)

IsAlphabetLoaded

public boolean IsAlphabetLoaded()

IsNuc

public boolean IsNuc(int i,
                     char c)

IsNuc

public boolean IsNuc(int i,
                     char c,
                     datatable data)

IsThermoDataLoaded

public boolean IsThermoDataLoaded()

openct

public int openct(java.lang.String ctfile)

opendbn

public int opendbn(java.lang.String bracketFile)

openseq

public int openseq(java.lang.String seqfile)

openseqx

public int openseqx(java.lang.String seqfile)

ProblemwithStructures

public boolean ProblemwithStructures()

ReadExperimentalPairBonus

public int ReadExperimentalPairBonus(java.lang.String filename)

ReadExperimentalPairBonus

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

ReadExperimentalPairBonus

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

ReadOffset

public int ReadOffset(java.lang.String SSOffset,
                      java.lang.String DSOffset)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename)

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     float SingleStrandThreshold,
                     float ModificationThreshold)

ReadSHAPE

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

ReadSHAPE

public int ReadSHAPE(java.lang.String filename,
                     RestraintType modifier,
                     boolean calculatePseudoEnergies)

RemoveAllStructures

public void RemoveAllStructures()

RemoveConstraints

public void RemoveConstraints()

RemoveEnergyLabels

public void RemoveEnergyLabels()

RemoveEnergyLabels

public void RemoveEnergyLabels(java.lang.String customLabel)

RemoveLastStructure

public void RemoveLastStructure()

RemovePair

public void RemovePair(int i)

RemovePair

public void RemovePair(int i,
                       int structurenumber)

RemoveStructure

public void RemoveStructure(int structurenumber)

SetCtLabel

public void SetCtLabel(java.lang.String label,
                       int structurenumber)

SetEnergy

public void SetEnergy(int structurenumber,
                      int energy)

SetPair

public void SetPair(int i,
                    int j)

SetPair

public void SetPair(int i,
                    int j,
                    int structurenumber)

SetPairingDistance

public void SetPairingDistance(int maxdistance)

SetSequence

public int SetSequence(java.lang.String sequence)

SetSequenceLabel

public void SetSequenceLabel(java.lang.String label)

setSHAPEFileRead

public void setSHAPEFileRead(boolean value)

setShowWarnings

public static void setShowWarnings(int value)

setSumShapeRepeats

public static void setSumShapeRepeats(boolean value)

SetThermodynamicDataTable

public void SetThermodynamicDataTable(datatable DataTablePointer)

sort

public void sort()

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)

writeseq

public int writeseq(java.lang.String seqfile)

writeseq

public int writeseq(java.lang.String seqfile,
                    int seqFileType)

writeseq

public int writeseq(java.lang.String seqfile,
                    int seqFileType,
                    boolean append)

WriteSHAPE

public int WriteSHAPE(java.lang.String outfile)

WriteSHAPE

public int WriteSHAPE(java.lang.String outfile,
                      boolean printHeaders)