ur_rna.RNAstructure.backend

Class RNABackendJNI

java.lang.Object

ur_rna.RNAstructure.backend.RNABackendJNI

public class RNABackendJNI
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
RNABackendJNI()

Method Summary

Modifier and Type	Method and Description
static void	CDblVector_add(long jarg1, CDblVector jarg1_, double jarg2)
static long	CDblVector_capacity(long jarg1, CDblVector jarg1_)
static void	CDblVector_clear(long jarg1, CDblVector jarg1_)
static double	CDblVector_get(long jarg1, CDblVector jarg1_, int jarg2)
static boolean	CDblVector_isEmpty(long jarg1, CDblVector jarg1_)
static void	CDblVector_reserve(long jarg1, CDblVector jarg1_, long jarg2)
static void	CDblVector_set(long jarg1, CDblVector jarg1_, int jarg2, double jarg3)
static long	CDblVector_size(long jarg1, CDblVector jarg1_)
static void	CIntVector_add(long jarg1, CIntVector jarg1_, int jarg2)
static long	CIntVector_capacity(long jarg1, CIntVector jarg1_)
static void	CIntVector_clear(long jarg1, CIntVector jarg1_)
static int	CIntVector_get(long jarg1, CIntVector jarg1_, int jarg2)
static boolean	CIntVector_isEmpty(long jarg1, CIntVector jarg1_)
static void	CIntVector_reserve(long jarg1, CIntVector jarg1_, long jarg2)
static void	CIntVector_set(long jarg1, CIntVector jarg1_, int jarg2, int jarg3)
static long	CIntVector_size(long jarg1, CIntVector jarg1_)
static int	COMPOUNDMESSAGELENGTH_get()
static int	DBN_BIT_MULTI_SEQ_get()
static int	DBN_BIT_MULTI_TITLE_get()
static int	DBN_BIT_SEQ_LABEL_get()
static int	DBN_BIT_SIDE_TITLES_get()
static int	DBN_FMT_MULTI_TITLE_AND_SEQ_get()
static int	DBN_FMT_MULTI_TITLE_get()
static int	DBN_FMT_SIDE_TITLES_get()
static int	DBN_FMT_SINGLE_TITLE_get()
static double	DEFAULT_SHAPE_INTERCEPT_get()
static double	DEFAULT_SHAPE_SLOPE_get()
static void	delete_CDblVector(long jarg1)
static void	delete_CIntVector(long jarg1)
static void	delete_datatable(long jarg1)
static void	delete_Dynalign_object(long jarg1)
static void	delete_HybridRNA(long jarg1)
static void	delete_PartialProgress(long jarg1)
static void	delete_ProgressHandler(long jarg1)
static void	delete_RNA(long jarg1)
static void	delete_SimpleProgressHandler(long jarg1)
static void	delete_singlestructure(long jarg1)
static void	delete_structure(long jarg1)
static void	delete_Thermodynamics(long jarg1)
static void	delete_TProgressDialog(long jarg1)
static void	delete_TwoRNA(long jarg1)
static int	Dynalign_object_Dynalign__SWIG_0(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9, boolean jarg10, short jarg11, boolean jarg12, short jarg13, int jarg14)
static int	Dynalign_object_Dynalign__SWIG_1(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9, boolean jarg10, short jarg11, boolean jarg12, short jarg13)
static int	Dynalign_object_Dynalign__SWIG_10(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4)
static int	Dynalign_object_Dynalign__SWIG_11(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3)
static int	Dynalign_object_Dynalign__SWIG_12(long jarg1, Dynalign_object jarg1_, short jarg2)
static int	Dynalign_object_Dynalign__SWIG_13(long jarg1, Dynalign_object jarg1_)
static int	Dynalign_object_Dynalign__SWIG_2(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9, boolean jarg10, short jarg11, boolean jarg12)
static int	Dynalign_object_Dynalign__SWIG_3(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9, boolean jarg10, short jarg11)
static int	Dynalign_object_Dynalign__SWIG_4(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9, boolean jarg10)
static int	Dynalign_object_Dynalign__SWIG_5(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8, java.lang.String jarg9)
static int	Dynalign_object_Dynalign__SWIG_6(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7, boolean jarg8)
static int	Dynalign_object_Dynalign__SWIG_7(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7)
static int	Dynalign_object_Dynalign__SWIG_8(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6)
static int	Dynalign_object_Dynalign__SWIG_9(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5)
static int	Dynalign_object_ForceAlignment(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3)
static double	Dynalign_object_GetBestPairEnergy(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3, int jarg4)
static java.lang.String	Dynalign_object_GetErrorMessage(long jarg1, Dynalign_object jarg1_, int jarg2)
static int	Dynalign_object_GetForcedAlignment(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3)
static double	Dynalign_object_GetLowestEnergy(long jarg1, Dynalign_object jarg1_)
static int	Dynalign_object_ReadAlignmentConstraints(long jarg1, Dynalign_object jarg1_, java.lang.String jarg2)
static void	Dynalign_object_SetProgress(long jarg1, Dynalign_object jarg1_, long jarg2, ProgressHandler jarg2_)
static void	Dynalign_object_StopProgress(long jarg1, Dynalign_object jarg1_)
static long	Dynalign_object_SWIGUpcast(long jarg1)
static int	Dynalign_object_Templatefromct(long jarg1, Dynalign_object jarg1_, java.lang.String jarg2)
static int	Dynalign_object_Templatefromdsv(long jarg1, Dynalign_object jarg1_, java.lang.String jarg2, float jarg3)
static void	Dynalign_object_WriteAlignment(long jarg1, Dynalign_object jarg1_, java.lang.String jarg2)
static int	FILE_CT_get()
static int	FILE_DBN_get()
static int	FILE_PFS_get()
static int	FILE_SAV_get()
static int	FILE_SEQ_get()
static void	findPseudoknots__SWIG_0(long jarg1, CIntVector jarg1_, long jarg2, CIntVector jarg2_, long jarg3, CIntVector jarg3_)
static void	findPseudoknots__SWIG_1(long jarg1, CIntVector jarg1_, long jarg2, CIntVector jarg2_)
static void	findPseudoknots__SWIG_2(long jarg1, CIntVector jarg1_)
static java.lang.String	getDataPath__SWIG_0(java.lang.String jarg1)
static java.lang.String	getDataPath__SWIG_1()
static boolean	hasPseudoknots(long jarg1, CIntVector jarg1_)
static int	HybridRNA_AccessFold__SWIG_0(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4, int jarg5, int jarg6)
static int	HybridRNA_AccessFold__SWIG_1(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4, int jarg5)
static int	HybridRNA_AccessFold__SWIG_2(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4)
static int	HybridRNA_AccessFold__SWIG_3(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3)
static int	HybridRNA_AccessFold__SWIG_4(long jarg1, HybridRNA jarg1_, double jarg2)
static int	HybridRNA_AccessFold__SWIG_5(long jarg1, HybridRNA jarg1_)
static int	HybridRNA_FoldBimolecular__SWIG_0(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5, int jarg6)
static int	HybridRNA_FoldBimolecular__SWIG_1(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5)
static int	HybridRNA_FoldBimolecular__SWIG_2(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4)
static int	HybridRNA_FoldBimolecular__SWIG_3(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3)
static int	HybridRNA_FoldBimolecular__SWIG_4(long jarg1, HybridRNA jarg1_, float jarg2)
static int	HybridRNA_FoldBimolecular__SWIG_5(long jarg1, HybridRNA jarg1_)
static int	HybridRNA_FoldDuplex__SWIG_0(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, int jarg5)
static int	HybridRNA_FoldDuplex__SWIG_1(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4)
static int	HybridRNA_FoldDuplex__SWIG_2(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3)
static int	HybridRNA_FoldDuplex__SWIG_3(long jarg1, HybridRNA jarg1_, float jarg2)
static int	HybridRNA_FoldDuplex__SWIG_4(long jarg1, HybridRNA jarg1_)
static int	HybridRNA_GetErrorCode(long jarg1, HybridRNA jarg1_)
static boolean	HybridRNA_GetForbidIntramolecular(long jarg1, HybridRNA jarg1_)
static java.lang.String	HybridRNA_GetMyErrorMessage(long jarg1, HybridRNA jarg1_, int jarg2)
static long	HybridRNA_GetRNA1(long jarg1, HybridRNA jarg1_)
static long	HybridRNA_GetRNA2(long jarg1, HybridRNA jarg1_)
static int	HybridRNA_PartitionFunctionBimolecular__SWIG_0(long jarg1, HybridRNA jarg1_, java.lang.String jarg2)
static int	HybridRNA_PartitionFunctionBimolecular__SWIG_1(long jarg1, HybridRNA jarg1_)
static void	HybridRNA_SetForbidIntramolecular(long jarg1, HybridRNA jarg1_, boolean jarg2)
static void	HybridRNA_SetProgress(long jarg1, HybridRNA jarg1_, long jarg2, ProgressHandler jarg2_)
static void	HybridRNA_StopProgress(long jarg1, HybridRNA jarg1_)
static long	HybridRNA_SWIGUpcast(long jarg1)
static long	new_CDblVector__SWIG_0()
static long	new_CDblVector__SWIG_1(long jarg1)
static long	new_CIntVector__SWIG_0()
static long	new_CIntVector__SWIG_1(long jarg1)
static long	new_datatable()
static long	new_Dynalign_object__SWIG_0()
static long	new_Dynalign_object__SWIG_1(java.lang.String jarg1, java.lang.String jarg2, boolean jarg3)
static long	new_Dynalign_object__SWIG_2(java.lang.String jarg1, java.lang.String jarg2)
static long	new_Dynalign_object__SWIG_3(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, boolean jarg5)
static long	new_Dynalign_object__SWIG_4(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4)
static long	new_Dynalign_object__SWIG_5(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, long jarg5, Thermodynamics jarg5_)
static long	new_Dynalign_object__SWIG_6(java.lang.String jarg1)
static long	new_Dynalign_object__SWIG_7(java.lang.String jarg1, short jarg2, short jarg3, short jarg4, short jarg5)
static long	new_HybridRNA__SWIG_0(java.lang.String jarg1, java.lang.String jarg2, boolean jarg3)
static long	new_HybridRNA__SWIG_1(java.lang.String jarg1, java.lang.String jarg2)
static long	new_HybridRNA__SWIG_2(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, boolean jarg5)
static long	new_HybridRNA__SWIG_3(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4)
static long	new_HybridRNA__SWIG_4(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, java.lang.String jarg5)
static long	new_PartialProgress(long jarg1, ProgressHandler jarg1_)
static long	new_RNA__SWIG_0(java.lang.String jarg1, boolean jarg2)
static long	new_RNA__SWIG_1(java.lang.String jarg1)
static long	new_RNA__SWIG_2(java.lang.String jarg1, int jarg2, java.lang.String jarg3, boolean jarg4, boolean jarg5)
static long	new_RNA__SWIG_3(java.lang.String jarg1, int jarg2, java.lang.String jarg3, boolean jarg4)
static long	new_RNA__SWIG_4(java.lang.String jarg1, int jarg2, java.lang.String jarg3)
static long	new_RNA__SWIG_5(java.lang.String jarg1, int jarg2, long jarg3, Thermodynamics jarg3_)
static long	new_RNA__SWIG_6(java.lang.String jarg1, int jarg2, boolean jarg3)
static long	new_RNA__SWIG_7(java.lang.String jarg1, int jarg2)
static long	new_RNA__SWIG_8(boolean jarg1)
static long	new_RNA__SWIG_9()
static long	new_SimpleProgressHandler()
static long	new_singlestructure(int jarg1)
static long	new_structure__SWIG_0(int jarg1)
static long	new_structure__SWIG_1()
static long	new_Thermodynamics__SWIG_0(boolean jarg1, java.lang.String jarg2, double jarg3)
static long	new_Thermodynamics__SWIG_1(boolean jarg1, java.lang.String jarg2)
static long	new_Thermodynamics__SWIG_2(boolean jarg1)
static long	new_Thermodynamics__SWIG_3()
static long	new_Thermodynamics__SWIG_4(long jarg1, Thermodynamics jarg1_)
static long	new_TProgressDialog()
static long	new_TwoRNA__SWIG_0(java.lang.String jarg1, java.lang.String jarg2, boolean jarg3)
static long	new_TwoRNA__SWIG_1(java.lang.String jarg1, java.lang.String jarg2)
static long	new_TwoRNA__SWIG_2(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, boolean jarg5)
static long	new_TwoRNA__SWIG_3(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4)
static long	new_TwoRNA__SWIG_4(java.lang.String jarg1, int jarg2, java.lang.String jarg3, int jarg4, long jarg5, Thermodynamics jarg5_)
static long	new_TwoRNA__SWIG_5()
static void	PartialProgress_advanceToNextStep(long jarg1, PartialProgress jarg1_, int jarg2)
static void	PartialProgress_cancel(long jarg1, PartialProgress jarg1_)
static boolean	PartialProgress_canceled(long jarg1, PartialProgress jarg1_)
static void	PartialProgress_setClient(long jarg1, PartialProgress jarg1_, long jarg2, ProgressHandler jarg2_)
static void	PartialProgress_setNextStep(long jarg1, PartialProgress jarg1_, int jarg2)
static void	PartialProgress_setWorkComplete(long jarg1, PartialProgress jarg1_, int jarg2)
static void	PartialProgress_stepComplete(long jarg1, PartialProgress jarg1_)
static long	PartialProgress_SWIGUpcast(long jarg1)
static void	PartialProgress_update(long jarg1, PartialProgress jarg1_, int jarg2)
static int	PartialProgress_workInNextStep_get(long jarg1, PartialProgress jarg1_)
static void	PartialProgress_workInNextStep_set(long jarg1, PartialProgress jarg1_, int jarg2)
static void	ProgressHandler_cancel(long jarg1, ProgressHandler jarg1_)
static boolean	ProgressHandler_canceled(long jarg1, ProgressHandler jarg1_)
static int	ProgressHandler_progress(long jarg1, ProgressHandler jarg1_)
static void	ProgressHandler_reset(long jarg1, ProgressHandler jarg1_)
static void	ProgressHandler_update__SWIG_0(long jarg1, ProgressHandler jarg1_, int jarg2)
static void	ProgressHandler_update__SWIG_1(long jarg1, ProgressHandler jarg1_, double jarg2, double jarg3)
static void	ProgressHandler_updateFraction(long jarg1, ProgressHandler jarg1_, double jarg2)
static int	RNA_AddComment__SWIG_0(long jarg1, RNA jarg1_, java.lang.String jarg2, int jarg3)
static int	RNA_AddComment__SWIG_1(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_BreakPseudoknot__SWIG_0(long jarg1, RNA jarg1_, boolean jarg2, int jarg3, boolean jarg4)
static int	RNA_BreakPseudoknot__SWIG_1(long jarg1, RNA jarg1_, boolean jarg2, int jarg3)
static int	RNA_BreakPseudoknot__SWIG_2(long jarg1, RNA jarg1_, boolean jarg2)
static int	RNA_BreakPseudoknot__SWIG_3(long jarg1, RNA jarg1_)
static double	RNA_CalculateFreeEnergy__SWIG_0(long jarg1, RNA jarg1_, int jarg2, boolean jarg3)
static double	RNA_CalculateFreeEnergy__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static double	RNA_CalculateFreeEnergy__SWIG_2(long jarg1, RNA jarg1_)
static boolean	RNA_ContainsPseudoknot(long jarg1, RNA jarg1_, int jarg2)
static void	RNA_CopyThermo(long jarg1, RNA jarg1_, long jarg2, Thermodynamics jarg2_)
static int	RNA_DetermineDrawingCoordinates__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, int jarg4)
static int	RNA_DetermineDrawingCoordinates__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static void	RNA_EnsureStructureCapcacity(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_FoldSingleStrand__SWIG_0(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5, int jarg6, boolean jarg7, boolean jarg8, boolean jarg9)
static int	RNA_FoldSingleStrand__SWIG_1(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5, int jarg6, boolean jarg7, boolean jarg8)
static int	RNA_FoldSingleStrand__SWIG_2(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5, int jarg6, boolean jarg7)
static int	RNA_FoldSingleStrand__SWIG_3(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5, int jarg6)
static int	RNA_FoldSingleStrand__SWIG_4(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, java.lang.String jarg5)
static int	RNA_FoldSingleStrand__SWIG_5(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4)
static int	RNA_FoldSingleStrand__SWIG_6(long jarg1, RNA jarg1_, float jarg2, int jarg3)
static int	RNA_FoldSingleStrand__SWIG_7(long jarg1, RNA jarg1_, float jarg2)
static int	RNA_FoldSingleStrand__SWIG_8(long jarg1, RNA jarg1_)
static int	RNA_ForceDoubleStranded(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ForceFMNCleavage(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ForceMaximumPairingDistance(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ForceModification(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ForcePair(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_ForceProhibitPair(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_ForceSingleStranded(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GenerateAllSuboptimalStructures__SWIG_0(long jarg1, RNA jarg1_, float jarg2, double jarg3)
static int	RNA_GenerateAllSuboptimalStructures__SWIG_1(long jarg1, RNA jarg1_, float jarg2)
static int	RNA_GenerateAllSuboptimalStructures__SWIG_2(long jarg1, RNA jarg1_)
static boolean	RNA_GetBackboneType(long jarg1, RNA jarg1_)
static java.lang.String	RNA_GetCommentString__SWIG_0(long jarg1, RNA jarg1_, int jarg2)
static java.lang.String	RNA_GetCommentString__SWIG_1(long jarg1, RNA jarg1_)
static double	RNA_GetEnsembleDefect__SWIG_0(long jarg1, RNA jarg1_, int jarg2)
static double	RNA_GetEnsembleDefect__SWIG_1(long jarg1, RNA jarg1_)
static double	RNA_GetEnsembleEnergy(long jarg1, RNA jarg1_)
static int	RNA_GetErrorCode(long jarg1, RNA jarg1_)
static java.lang.String	RNA_GetErrorDetails(long jarg1, RNA jarg1_)
static java.lang.String	RNA_GetErrorMessage(int jarg1)
static int	RNA_GetForcedDoubleStranded(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetForcedFMNCleavage(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetForcedModification(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetForcedPair(long jarg1, RNA jarg1_, int jarg2, boolean jarg3)
static int	RNA_GetForcedProhibitedPair(long jarg1, RNA jarg1_, int jarg2, boolean jarg3)
static int	RNA_GetForcedSingleStranded(long jarg1, RNA jarg1_, int jarg2)
static double	RNA_GetFreeEnergy(long jarg1, RNA jarg1_, int jarg2)
static java.lang.String	RNA_GetFullErrorMessage(long jarg1, RNA jarg1_)
static int	RNA_getIntAt(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_getInts(long jarg1, RNA jarg1_, int[] jarg2, int jarg3)
static int	RNA_GetLabelXCoordinate(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetLabelYCoordinate(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetMaximumPairingDistance(long jarg1, RNA jarg1_)
static char	RNA_GetNucleotide(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetNucleotideXCoordinate(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetNucleotideYCoordinate(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_GetNumberOfForcedDoubleStranded(long jarg1, RNA jarg1_)
static int	RNA_GetNumberOfForcedFMNCleavages(long jarg1, RNA jarg1_)
static int	RNA_GetNumberOfForcedModifications(long jarg1, RNA jarg1_)
static int	RNA_GetNumberOfForcedPairs(long jarg1, RNA jarg1_)
static int	RNA_GetNumberOfForcedProhibitedPairs(long jarg1, RNA jarg1_)
static int	RNA_GetNumberOfForcedSingleStranded(long jarg1, RNA jarg1_)
static int	RNA_GetPair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_GetPair__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static double	RNA_GetPairEnergy(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_GetPairProbabilities(long jarg1, RNA jarg1_, double[] jarg2, int jarg3)
static double	RNA_GetPairProbability(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static long	RNA_GetProgress(long jarg1, RNA jarg1_)
static java.lang.String	RNA_GetSequence(long jarg1, RNA jarg1_)
static int	RNA_GetSequenceLength(long jarg1, RNA jarg1_)
static long	RNA_GetStructure(long jarg1, RNA jarg1_)
static int	RNA_GetStructureNumber(long jarg1, RNA jarg1_)
static void	RNA_initInts(long jarg1, RNA jarg1_)
static int	RNA_MaximizeExpectedAccuracy__SWIG_0(long jarg1, RNA jarg1_, double jarg2, int jarg3, int jarg4, double jarg5)
static int	RNA_MaximizeExpectedAccuracy__SWIG_1(long jarg1, RNA jarg1_, double jarg2, int jarg3, int jarg4)
static int	RNA_MaximizeExpectedAccuracy__SWIG_2(long jarg1, RNA jarg1_, double jarg2, int jarg3)
static int	RNA_MaximizeExpectedAccuracy__SWIG_3(long jarg1, RNA jarg1_, double jarg2)
static int	RNA_MaximizeExpectedAccuracy__SWIG_4(long jarg1, RNA jarg1_)
static int	RNA_PartitionFunction__SWIG_0(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, boolean jarg4, boolean jarg5)
static int	RNA_PartitionFunction__SWIG_1(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, boolean jarg4)
static int	RNA_PartitionFunction__SWIG_2(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3)
static int	RNA_PartitionFunction__SWIG_3(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_PartitionFunction__SWIG_4(long jarg1, RNA jarg1_)
static int	RNA_PredictProbablePairs__SWIG_0(long jarg1, RNA jarg1_, float jarg2)
static int	RNA_PredictProbablePairs__SWIG_1(long jarg1, RNA jarg1_)
static int	RNA_ProbKnot__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_ProbKnot__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ProbKnot__SWIG_2(long jarg1, RNA jarg1_)
static int	RNA_ProbKnotFromSample__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_ProbKnotFromSample__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_ProbKnotFromSample__SWIG_2(long jarg1, RNA jarg1_)
static int	RNA_ReadConstraints(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_ReadDMS(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_ReadDSO(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_ReadExperimentalPairBonus(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4)
static int	RNA_ReadSHAPE__SWIG_0(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4, int jarg5, boolean jarg6)
static int	RNA_ReadSHAPE__SWIG_1(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4, int jarg5)
static int	RNA_ReadSHAPE__SWIG_2(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4)
static int	RNA_ReadSHAPE__SWIG_3(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4, double jarg5, double jarg6, int jarg7)
static int	RNA_ReadSHAPE__SWIG_4(long jarg1, RNA jarg1_, java.lang.String jarg2, double jarg3, double jarg4, double jarg5, double jarg6)
static int	RNA_ReadSSO(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_ReFoldSingleStrand__SWIG_0(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4)
static int	RNA_ReFoldSingleStrand__SWIG_1(long jarg1, RNA jarg1_, float jarg2, int jarg3)
static int	RNA_ReFoldSingleStrand__SWIG_2(long jarg1, RNA jarg1_, float jarg2)
static int	RNA_ReFoldSingleStrand__SWIG_3(long jarg1, RNA jarg1_)
static int	RNA_RemoveBasePair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_RemoveBasePair__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static void	RNA_RemoveConstraints(long jarg1, RNA jarg1_)
static int	RNA_RemovePairs__SWIG_0(long jarg1, RNA jarg1_, int jarg2, boolean jarg3)
static int	RNA_RemovePairs__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_RemovePairs__SWIG_2(long jarg1, RNA jarg1_)
static void	RNA_ResetError(long jarg1, RNA jarg1_)
static void	RNA_SetErrorDetails(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_SetExtrinsic(long jarg1, RNA jarg1_, int jarg2, int jarg3, double jarg4)
static void	RNA_SetProgress(long jarg1, RNA jarg1_, long jarg2, ProgressHandler jarg2_)
static int	RNA_SpecifyPair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, int jarg4)
static int	RNA_SpecifyPair__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_Stochastic__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3)
static int	RNA_Stochastic__SWIG_1(long jarg1, RNA jarg1_, int jarg2)
static int	RNA_Stochastic__SWIG_2(long jarg1, RNA jarg1_)
static void	RNA_StopProgress(long jarg1, RNA jarg1_)
static long	RNA_SWIGUpcast(long jarg1)
static int	RNA_WriteConstraints(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_WriteCt(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_WriteDotBracket__SWIG_0(long jarg1, RNA jarg1_, java.lang.String jarg2, int jarg3, int jarg4)
static int	RNA_WriteDotBracket__SWIG_1(long jarg1, RNA jarg1_, java.lang.String jarg2, int jarg3)
static int	RNA_WriteDotBracket__SWIG_2(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	RNA_WriteThermodynamicDetails__SWIG_0(long jarg1, RNA jarg1_, java.lang.String jarg2, boolean jarg3)
static int	RNA_WriteThermodynamicDetails__SWIG_1(long jarg1, RNA jarg1_, java.lang.String jarg2)
static int	SEQUENCE_STRING_get()
static void	setDataPath(java.lang.String jarg1)
static long	SimpleProgressHandler_SWIGUpcast(long jarg1)
static java.lang.String	singlestructure_ctlabel_get(long jarg1, singlestructure jarg1_)
static void	singlestructure_ctlabel_set(long jarg1, singlestructure jarg1_, java.lang.String jarg2)
static int	singlestructure_energy_get(long jarg1, singlestructure jarg1_)
static void	singlestructure_energy_set(long jarg1, singlestructure jarg1_, int jarg2)
static int	singlestructure_getBasePair(long jarg1, singlestructure jarg1_, int jarg2)
static int	singlestructure_getSequenceLength(long jarg1, singlestructure jarg1_)
static void	singlestructure_setBasePair(long jarg1, singlestructure jarg1_, int jarg2, int jarg3)
static void	singlestructure_setSequenceLength(long jarg1, singlestructure jarg1_, int jarg2)
static void	structure_AddDouble(long jarg1, structure jarg1_, int jarg2)
static void	structure_AddForbiddenPair(long jarg1, structure jarg1_, int jarg2, int jarg3)
static void	structure_AddGUPair(long jarg1, structure jarg1_, int jarg2)
static void	structure_AddModified(long jarg1, structure jarg1_, int jarg2)
static void	structure_AddPair(long jarg1, structure jarg1_, int jarg2, int jarg3)
static void	structure_AddSingle(long jarg1, structure jarg1_, int jarg2)
static void	structure_AddStructure(long jarg1, structure jarg1_)
static void	structure_allocateconstant(long jarg1, structure jarg1_)
static void	structure_AllocateSHAPE(long jarg1, structure jarg1_)
static void	structure_allocatetem(long jarg1, structure jarg1_)
static void	structure_BreakPseudoknots(long jarg1, structure jarg1_, int jarg2)
static void	structure_CleanStructure(long jarg1, structure jarg1_, int jarg2)
static int	structure_ctout(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	structure_DeleteSHAPE(long jarg1, structure jarg1_)
static boolean	structure_DistanceLimited(long jarg1, structure jarg1_)
static void	structure_FindPseudoknots__SWIG_0(long jarg1, structure jarg1_, int jarg2, long jarg3, CIntVector jarg3_, long jarg4, CIntVector jarg4_)
static void	structure_FindPseudoknots__SWIG_1(long jarg1, structure jarg1_, int jarg2, long jarg3, CIntVector jarg3_)
static void	structure_FindPseudoknots__SWIG_2(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetBase(long jarg1, structure jarg1_, int jarg2)
static java.lang.String	structure_GetCtLabel(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetDouble(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetEnergy(long jarg1, structure jarg1_, int jarg2)
static java.lang.String	structure_GetErrorDetails(long jarg1, structure jarg1_)
static int	structure_GetForbiddenPair3(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetForbiddenPair5(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetGUpair(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetModified(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetNumberofDoubles(long jarg1, structure jarg1_)
static int	structure_GetNumberofForbiddenPairs(long jarg1, structure jarg1_)
static int	structure_GetNumberofGU(long jarg1, structure jarg1_)
static int	structure_GetNumberofModified(long jarg1, structure jarg1_)
static int	structure_GetNumberofPairs(long jarg1, structure jarg1_)
static int	structure_GetNumberofSingles(long jarg1, structure jarg1_)
static int	structure_GetNumberofStructures(long jarg1, structure jarg1_)
static int	structure_GetPair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3)
static int	structure_GetPair__SWIG_1(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetPair3(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetPair5(long jarg1, structure jarg1_, int jarg2)
static int	structure_GetPairingDistanceLimit(long jarg1, structure jarg1_)
static void	structure_GetPseudoknotRanks__SWIG_0(long jarg1, structure jarg1_, long jarg2, CIntVector jarg2_, int jarg3)
static void	structure_GetPseudoknotRanks__SWIG_1(long jarg1, structure jarg1_, long jarg2, CIntVector jarg2_)
static java.lang.String	structure_GetSequence(long jarg1, structure jarg1_)
static java.lang.String	structure_GetSequenceLabel(long jarg1, structure jarg1_)
static int	structure_GetSequenceLength(long jarg1, structure jarg1_)
static int	structure_GetSingle(long jarg1, structure jarg1_, int jarg2)
static long	structure_GetThermodynamicDataTable(long jarg1, structure jarg1_)
static boolean	structure_HasPseudoknots__SWIG_0(long jarg1, structure jarg1_, int jarg2)
static boolean	structure_HasPseudoknots__SWIG_1(long jarg1, structure jarg1_)
static boolean	structure_IsAlphabetLoaded(long jarg1, structure jarg1_)
static boolean	structure_IsNuc__SWIG_0(long jarg1, structure jarg1_, int jarg2, char jarg3)
static boolean	structure_IsNuc__SWIG_1(long jarg1, structure jarg1_, int jarg2, char jarg3, long jarg4, datatable jarg4_)
static boolean	structure_IsThermoDataLoaded(long jarg1, structure jarg1_)
static double	structure_kT_get()
static int	structure_openct(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_opendbn(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_openseq(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_openseqx(long jarg1, structure jarg1_, java.lang.String jarg2)
static boolean	structure_ProblemwithStructures(long jarg1, structure jarg1_)
static int	structure_ReadExperimentalPairBonus__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2, double jarg3, double jarg4)
static int	structure_ReadExperimentalPairBonus__SWIG_1(long jarg1, structure jarg1_, java.lang.String jarg2, double jarg3)
static int	structure_ReadExperimentalPairBonus__SWIG_2(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_ReadOffset(long jarg1, structure jarg1_, java.lang.String jarg2, java.lang.String jarg3)
static int	structure_ReadSHAPE__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2, float jarg3, float jarg4)
static int	structure_ReadSHAPE__SWIG_1(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3, boolean jarg4)
static int	structure_ReadSHAPE__SWIG_2(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3)
static int	structure_ReadSHAPE__SWIG_3(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	structure_RemoveAllStructures(long jarg1, structure jarg1_)
static void	structure_RemoveConstraints(long jarg1, structure jarg1_)
static void	structure_RemoveEnergyLabels__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	structure_RemoveEnergyLabels__SWIG_1(long jarg1, structure jarg1_)
static void	structure_RemoveLastStructure(long jarg1, structure jarg1_)
static void	structure_RemovePair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3)
static void	structure_RemovePair__SWIG_1(long jarg1, structure jarg1_, int jarg2)
static void	structure_RemoveStructure(long jarg1, structure jarg1_, int jarg2)
static void	structure_SetCtLabel(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3)
static void	structure_SetEnergy(long jarg1, structure jarg1_, int jarg2, int jarg3)
static void	structure_SetPair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3, int jarg4)
static void	structure_SetPair__SWIG_1(long jarg1, structure jarg1_, int jarg2, int jarg3)
static void	structure_SetPairingDistance(long jarg1, structure jarg1_, int jarg2)
static int	structure_SetSequence(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	structure_SetSequenceLabel(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	structure_SetThermodynamicDataTable(long jarg1, structure jarg1_, long jarg2, datatable jarg2_)
static boolean	structure_SHAPEFileRead_get(long jarg1, structure jarg1_)
static void	structure_SHAPEFileRead_set(long jarg1, structure jarg1_, boolean jarg2)
static int	structure_ShowWarnings_get()
static void	structure_ShowWarnings_set(int jarg1)
static void	structure_sort(long jarg1, structure jarg1_)
static boolean	structure_SumShapeRepeats_get()
static void	structure_SumShapeRepeats_set(boolean jarg1)
static int	structure_writedotbracket__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3, int jarg4)
static int	structure_writedotbracket__SWIG_1(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3)
static int	structure_writedotbracket__SWIG_2(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_writeseq__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3, boolean jarg4)
static int	structure_writeseq__SWIG_1(long jarg1, structure jarg1_, java.lang.String jarg2, int jarg3)
static int	structure_writeseq__SWIG_2(long jarg1, structure jarg1_, java.lang.String jarg2)
static int	structure_WriteSHAPE__SWIG_0(long jarg1, structure jarg1_, java.lang.String jarg2, boolean jarg3)
static int	structure_WriteSHAPE__SWIG_1(long jarg1, structure jarg1_, java.lang.String jarg2)
static void	Thermodynamics_ClearEnergies(long jarg1, Thermodynamics jarg1_)
static void	Thermodynamics_ClearEnthalpies(long jarg1, Thermodynamics jarg1_)
static java.lang.String	Thermodynamics_GetAlphabetName(long jarg1, Thermodynamics jarg1_)
static long	Thermodynamics_GetDatatable(long jarg1, Thermodynamics jarg1_)
static boolean	Thermodynamics_GetEnergyRead(long jarg1, Thermodynamics jarg1_)
static long	Thermodynamics_GetEnthalpyTable__SWIG_0(long jarg1, Thermodynamics jarg1_, java.lang.String jarg2)
static long	Thermodynamics_GetEnthalpyTable__SWIG_1(long jarg1, Thermodynamics jarg1_)
static double	Thermodynamics_GetTemperature(long jarg1, Thermodynamics jarg1_)
static boolean	Thermodynamics_IsAlphabetRead(long jarg1, Thermodynamics jarg1_)
static boolean	Thermodynamics_isrna_get(long jarg1, Thermodynamics jarg1_)
static void	Thermodynamics_isrna_set(long jarg1, Thermodynamics jarg1_, boolean jarg2)
static int	Thermodynamics_ReadThermodynamic__SWIG_0(long jarg1, Thermodynamics jarg1_, java.lang.String jarg2, java.lang.String jarg3, double jarg4)
static int	Thermodynamics_ReadThermodynamic__SWIG_1(long jarg1, Thermodynamics jarg1_, java.lang.String jarg2, java.lang.String jarg3)
static int	Thermodynamics_ReadThermodynamic__SWIG_2(long jarg1, Thermodynamics jarg1_, java.lang.String jarg2)
static int	Thermodynamics_ReadThermodynamic__SWIG_3(long jarg1, Thermodynamics jarg1_)
static int	Thermodynamics_ReloadDataTables__SWIG_0(long jarg1, Thermodynamics jarg1_, double jarg2)
static int	Thermodynamics_ReloadDataTables__SWIG_1(long jarg1, Thermodynamics jarg1_)
static int	Thermodynamics_SetTemperature(long jarg1, Thermodynamics jarg1_, double jarg2)
static boolean	Thermodynamics_VerifyThermodynamic(long jarg1, Thermodynamics jarg1_)
static long	TProgressDialog_SWIGUpcast(long jarg1)
static void	TProgressDialog_update(long jarg1, TProgressDialog jarg1_, int jarg2)
static java.lang.String	TwoRNA_compoundmessage_get(long jarg1, TwoRNA jarg1_)
static void	TwoRNA_compoundmessage_set(long jarg1, TwoRNA jarg1_, java.lang.String jarg2)
static int	TwoRNA_GetErrorCode(long jarg1, TwoRNA jarg1_)
static java.lang.String	TwoRNA_GetErrorDetails(long jarg1, TwoRNA jarg1_)
static java.lang.String	TwoRNA_GetErrorMessage(long jarg1, TwoRNA jarg1_, int jarg2)
static java.lang.String	TwoRNA_GetErrorMessageString(long jarg1, TwoRNA jarg1_, int jarg2)
static long	TwoRNA_GetRNA1(long jarg1, TwoRNA jarg1_)
static long	TwoRNA_GetRNA2(long jarg1, TwoRNA jarg1_)
static double	TwoRNA_GetTemperature(long jarg1, TwoRNA jarg1_)
static void	TwoRNA_ResetError(long jarg1, TwoRNA jarg1_)
static void	TwoRNA_SetErrorDetails(long jarg1, TwoRNA jarg1_, java.lang.String jarg2)
static int	TwoRNA_SetTemperature(long jarg1, TwoRNA jarg1_, double jarg2)

Methods inherited from class java.lang.Object

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

Constructor Detail

RNABackendJNI

public RNABackendJNI()

Method Detail

CDblVector_add

public static final void CDblVector_add(long jarg1,
                                        CDblVector jarg1_,
                                        double jarg2)

CDblVector_capacity

public static final long CDblVector_capacity(long jarg1,
                                             CDblVector jarg1_)

CDblVector_clear

public static final void CDblVector_clear(long jarg1,
                                          CDblVector jarg1_)

CDblVector_get

public static final double CDblVector_get(long jarg1,
                                          CDblVector jarg1_,
                                          int jarg2)

CDblVector_isEmpty

public static final boolean CDblVector_isEmpty(long jarg1,
                                               CDblVector jarg1_)

CDblVector_reserve

public static final void CDblVector_reserve(long jarg1,
                                            CDblVector jarg1_,
                                            long jarg2)

CDblVector_set

public static final void CDblVector_set(long jarg1,
                                        CDblVector jarg1_,
                                        int jarg2,
                                        double jarg3)

CDblVector_size

public static final long CDblVector_size(long jarg1,
                                         CDblVector jarg1_)

CIntVector_add

public static final void CIntVector_add(long jarg1,
                                        CIntVector jarg1_,
                                        int jarg2)

CIntVector_capacity

public static final long CIntVector_capacity(long jarg1,
                                             CIntVector jarg1_)

CIntVector_clear

public static final void CIntVector_clear(long jarg1,
                                          CIntVector jarg1_)

CIntVector_get

public static final int CIntVector_get(long jarg1,
                                       CIntVector jarg1_,
                                       int jarg2)

CIntVector_isEmpty

public static final boolean CIntVector_isEmpty(long jarg1,
                                               CIntVector jarg1_)

CIntVector_reserve

public static final void CIntVector_reserve(long jarg1,
                                            CIntVector jarg1_,
                                            long jarg2)

CIntVector_set

public static final void CIntVector_set(long jarg1,
                                        CIntVector jarg1_,
                                        int jarg2,
                                        int jarg3)

CIntVector_size

public static final long CIntVector_size(long jarg1,
                                         CIntVector jarg1_)

COMPOUNDMESSAGELENGTH_get

public static final int COMPOUNDMESSAGELENGTH_get()

DBN_BIT_MULTI_SEQ_get

public static final int DBN_BIT_MULTI_SEQ_get()

DBN_BIT_MULTI_TITLE_get

public static final int DBN_BIT_MULTI_TITLE_get()

DBN_BIT_SEQ_LABEL_get

public static final int DBN_BIT_SEQ_LABEL_get()

DBN_BIT_SIDE_TITLES_get

public static final int DBN_BIT_SIDE_TITLES_get()

DBN_FMT_MULTI_TITLE_AND_SEQ_get

public static final int DBN_FMT_MULTI_TITLE_AND_SEQ_get()

DBN_FMT_MULTI_TITLE_get

public static final int DBN_FMT_MULTI_TITLE_get()

DBN_FMT_SIDE_TITLES_get

public static final int DBN_FMT_SIDE_TITLES_get()

DBN_FMT_SINGLE_TITLE_get

public static final int DBN_FMT_SINGLE_TITLE_get()

DEFAULT_SHAPE_INTERCEPT_get

public static final double DEFAULT_SHAPE_INTERCEPT_get()

DEFAULT_SHAPE_SLOPE_get

public static final double DEFAULT_SHAPE_SLOPE_get()

delete_CDblVector

public static final void delete_CDblVector(long jarg1)

delete_CIntVector

public static final void delete_CIntVector(long jarg1)

delete_datatable

public static final void delete_datatable(long jarg1)

delete_Dynalign_object

public static final void delete_Dynalign_object(long jarg1)

delete_HybridRNA

public static final void delete_HybridRNA(long jarg1)

delete_PartialProgress

public static final void delete_PartialProgress(long jarg1)

delete_ProgressHandler

public static final void delete_ProgressHandler(long jarg1)

delete_RNA

public static final void delete_RNA(long jarg1)

delete_SimpleProgressHandler

public static final void delete_SimpleProgressHandler(long jarg1)

delete_singlestructure

public static final void delete_singlestructure(long jarg1)

delete_structure

public static final void delete_structure(long jarg1)

delete_Thermodynamics

public static final void delete_Thermodynamics(long jarg1)

delete_TProgressDialog

public static final void delete_TProgressDialog(long jarg1)

delete_TwoRNA

public static final void delete_TwoRNA(long jarg1)

Dynalign_object_Dynalign__SWIG_0

public static final int Dynalign_object_Dynalign__SWIG_0(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9,
                                                         boolean jarg10,
                                                         short jarg11,
                                                         boolean jarg12,
                                                         short jarg13,
                                                         int jarg14)

Dynalign_object_Dynalign__SWIG_1

public static final int Dynalign_object_Dynalign__SWIG_1(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9,
                                                         boolean jarg10,
                                                         short jarg11,
                                                         boolean jarg12,
                                                         short jarg13)

Dynalign_object_Dynalign__SWIG_10

public static final int Dynalign_object_Dynalign__SWIG_10(long jarg1,
                                                          Dynalign_object jarg1_,
                                                          short jarg2,
                                                          short jarg3,
                                                          short jarg4)

Dynalign_object_Dynalign__SWIG_11

public static final int Dynalign_object_Dynalign__SWIG_11(long jarg1,
                                                          Dynalign_object jarg1_,
                                                          short jarg2,
                                                          short jarg3)

Dynalign_object_Dynalign__SWIG_12

public static final int Dynalign_object_Dynalign__SWIG_12(long jarg1,
                                                          Dynalign_object jarg1_,
                                                          short jarg2)

Dynalign_object_Dynalign__SWIG_13

public static final int Dynalign_object_Dynalign__SWIG_13(long jarg1,
                                                          Dynalign_object jarg1_)

Dynalign_object_Dynalign__SWIG_2

public static final int Dynalign_object_Dynalign__SWIG_2(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9,
                                                         boolean jarg10,
                                                         short jarg11,
                                                         boolean jarg12)

Dynalign_object_Dynalign__SWIG_3

public static final int Dynalign_object_Dynalign__SWIG_3(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9,
                                                         boolean jarg10,
                                                         short jarg11)

Dynalign_object_Dynalign__SWIG_4

public static final int Dynalign_object_Dynalign__SWIG_4(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9,
                                                         boolean jarg10)

Dynalign_object_Dynalign__SWIG_5

public static final int Dynalign_object_Dynalign__SWIG_5(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8,
                                                         java.lang.String jarg9)

Dynalign_object_Dynalign__SWIG_6

public static final int Dynalign_object_Dynalign__SWIG_6(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7,
                                                         boolean jarg8)

Dynalign_object_Dynalign__SWIG_7

public static final int Dynalign_object_Dynalign__SWIG_7(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6,
                                                         float jarg7)

Dynalign_object_Dynalign__SWIG_8

public static final int Dynalign_object_Dynalign__SWIG_8(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5,
                                                         short jarg6)

Dynalign_object_Dynalign__SWIG_9

public static final int Dynalign_object_Dynalign__SWIG_9(long jarg1,
                                                         Dynalign_object jarg1_,
                                                         short jarg2,
                                                         short jarg3,
                                                         short jarg4,
                                                         short jarg5)

Dynalign_object_ForceAlignment

public static final int Dynalign_object_ForceAlignment(long jarg1,
                                                       Dynalign_object jarg1_,
                                                       int jarg2,
                                                       int jarg3)

Dynalign_object_GetBestPairEnergy

public static final double Dynalign_object_GetBestPairEnergy(long jarg1,
                                                             Dynalign_object jarg1_,
                                                             int jarg2,
                                                             int jarg3,
                                                             int jarg4)

Dynalign_object_GetErrorMessage

public static final java.lang.String Dynalign_object_GetErrorMessage(long jarg1,
                                                                     Dynalign_object jarg1_,
                                                                     int jarg2)

Dynalign_object_GetForcedAlignment

public static final int Dynalign_object_GetForcedAlignment(long jarg1,
                                                           Dynalign_object jarg1_,
                                                           int jarg2,
                                                           int jarg3)

Dynalign_object_GetLowestEnergy

public static final double Dynalign_object_GetLowestEnergy(long jarg1,
                                                           Dynalign_object jarg1_)

Dynalign_object_ReadAlignmentConstraints

public static final int Dynalign_object_ReadAlignmentConstraints(long jarg1,
                                                                 Dynalign_object jarg1_,
                                                                 java.lang.String jarg2)

Dynalign_object_SetProgress

public static final void Dynalign_object_SetProgress(long jarg1,
                                                     Dynalign_object jarg1_,
                                                     long jarg2,
                                                     ProgressHandler jarg2_)

Dynalign_object_StopProgress

public static final void Dynalign_object_StopProgress(long jarg1,
                                                      Dynalign_object jarg1_)

Dynalign_object_SWIGUpcast

public static final long Dynalign_object_SWIGUpcast(long jarg1)

Dynalign_object_Templatefromct

public static final int Dynalign_object_Templatefromct(long jarg1,
                                                       Dynalign_object jarg1_,
                                                       java.lang.String jarg2)

Dynalign_object_Templatefromdsv

public static final int Dynalign_object_Templatefromdsv(long jarg1,
                                                        Dynalign_object jarg1_,
                                                        java.lang.String jarg2,
                                                        float jarg3)

Dynalign_object_WriteAlignment

public static final void Dynalign_object_WriteAlignment(long jarg1,
                                                        Dynalign_object jarg1_,
                                                        java.lang.String jarg2)

FILE_CT_get

public static final int FILE_CT_get()

FILE_DBN_get

public static final int FILE_DBN_get()

FILE_PFS_get

public static final int FILE_PFS_get()

FILE_SAV_get

public static final int FILE_SAV_get()

FILE_SEQ_get

public static final int FILE_SEQ_get()

findPseudoknots__SWIG_0

public static final void findPseudoknots__SWIG_0(long jarg1,
                                                 CIntVector jarg1_,
                                                 long jarg2,
                                                 CIntVector jarg2_,
                                                 long jarg3,
                                                 CIntVector jarg3_)

findPseudoknots__SWIG_1

public static final void findPseudoknots__SWIG_1(long jarg1,
                                                 CIntVector jarg1_,
                                                 long jarg2,
                                                 CIntVector jarg2_)

findPseudoknots__SWIG_2

public static final void findPseudoknots__SWIG_2(long jarg1,
                                                 CIntVector jarg1_)

getDataPath__SWIG_0

public static final java.lang.String getDataPath__SWIG_0(java.lang.String jarg1)

getDataPath__SWIG_1

public static final java.lang.String getDataPath__SWIG_1()

hasPseudoknots

public static final boolean hasPseudoknots(long jarg1,
                                           CIntVector jarg1_)

HybridRNA_AccessFold__SWIG_0

public static final int HybridRNA_AccessFold__SWIG_0(long jarg1,
                                                     HybridRNA jarg1_,
                                                     double jarg2,
                                                     float jarg3,
                                                     int jarg4,
                                                     int jarg5,
                                                     int jarg6)

HybridRNA_AccessFold__SWIG_1

public static final int HybridRNA_AccessFold__SWIG_1(long jarg1,
                                                     HybridRNA jarg1_,
                                                     double jarg2,
                                                     float jarg3,
                                                     int jarg4,
                                                     int jarg5)

HybridRNA_AccessFold__SWIG_2

public static final int HybridRNA_AccessFold__SWIG_2(long jarg1,
                                                     HybridRNA jarg1_,
                                                     double jarg2,
                                                     float jarg3,
                                                     int jarg4)

HybridRNA_AccessFold__SWIG_3

public static final int HybridRNA_AccessFold__SWIG_3(long jarg1,
                                                     HybridRNA jarg1_,
                                                     double jarg2,
                                                     float jarg3)

HybridRNA_AccessFold__SWIG_4

public static final int HybridRNA_AccessFold__SWIG_4(long jarg1,
                                                     HybridRNA jarg1_,
                                                     double jarg2)

HybridRNA_AccessFold__SWIG_5

public static final int HybridRNA_AccessFold__SWIG_5(long jarg1,
                                                     HybridRNA jarg1_)

HybridRNA_FoldBimolecular__SWIG_0

public static final int HybridRNA_FoldBimolecular__SWIG_0(long jarg1,
                                                          HybridRNA jarg1_,
                                                          float jarg2,
                                                          int jarg3,
                                                          int jarg4,
                                                          java.lang.String jarg5,
                                                          int jarg6)

HybridRNA_FoldBimolecular__SWIG_1

public static final int HybridRNA_FoldBimolecular__SWIG_1(long jarg1,
                                                          HybridRNA jarg1_,
                                                          float jarg2,
                                                          int jarg3,
                                                          int jarg4,
                                                          java.lang.String jarg5)

HybridRNA_FoldBimolecular__SWIG_2

public static final int HybridRNA_FoldBimolecular__SWIG_2(long jarg1,
                                                          HybridRNA jarg1_,
                                                          float jarg2,
                                                          int jarg3,
                                                          int jarg4)

HybridRNA_FoldBimolecular__SWIG_3

public static final int HybridRNA_FoldBimolecular__SWIG_3(long jarg1,
                                                          HybridRNA jarg1_,
                                                          float jarg2,
                                                          int jarg3)

HybridRNA_FoldBimolecular__SWIG_4

public static final int HybridRNA_FoldBimolecular__SWIG_4(long jarg1,
                                                          HybridRNA jarg1_,
                                                          float jarg2)

HybridRNA_FoldBimolecular__SWIG_5

public static final int HybridRNA_FoldBimolecular__SWIG_5(long jarg1,
                                                          HybridRNA jarg1_)

HybridRNA_FoldDuplex__SWIG_0

public static final int HybridRNA_FoldDuplex__SWIG_0(long jarg1,
                                                     HybridRNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     int jarg5)

HybridRNA_FoldDuplex__SWIG_1

public static final int HybridRNA_FoldDuplex__SWIG_1(long jarg1,
                                                     HybridRNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4)

HybridRNA_FoldDuplex__SWIG_2

public static final int HybridRNA_FoldDuplex__SWIG_2(long jarg1,
                                                     HybridRNA jarg1_,
                                                     float jarg2,
                                                     int jarg3)

HybridRNA_FoldDuplex__SWIG_3

public static final int HybridRNA_FoldDuplex__SWIG_3(long jarg1,
                                                     HybridRNA jarg1_,
                                                     float jarg2)

HybridRNA_FoldDuplex__SWIG_4

public static final int HybridRNA_FoldDuplex__SWIG_4(long jarg1,
                                                     HybridRNA jarg1_)

HybridRNA_GetErrorCode

public static final int HybridRNA_GetErrorCode(long jarg1,
                                               HybridRNA jarg1_)

HybridRNA_GetForbidIntramolecular

public static final boolean HybridRNA_GetForbidIntramolecular(long jarg1,
                                                              HybridRNA jarg1_)

HybridRNA_GetMyErrorMessage

public static final java.lang.String HybridRNA_GetMyErrorMessage(long jarg1,
                                                                 HybridRNA jarg1_,
                                                                 int jarg2)

HybridRNA_GetRNA1

public static final long HybridRNA_GetRNA1(long jarg1,
                                           HybridRNA jarg1_)

HybridRNA_GetRNA2

public static final long HybridRNA_GetRNA2(long jarg1,
                                           HybridRNA jarg1_)

HybridRNA_PartitionFunctionBimolecular__SWIG_0

public static final int HybridRNA_PartitionFunctionBimolecular__SWIG_0(long jarg1,
                                                                       HybridRNA jarg1_,
                                                                       java.lang.String jarg2)

HybridRNA_PartitionFunctionBimolecular__SWIG_1

public static final int HybridRNA_PartitionFunctionBimolecular__SWIG_1(long jarg1,
                                                                       HybridRNA jarg1_)

HybridRNA_SetForbidIntramolecular

public static final void HybridRNA_SetForbidIntramolecular(long jarg1,
                                                           HybridRNA jarg1_,
                                                           boolean jarg2)

HybridRNA_SetProgress

public static final void HybridRNA_SetProgress(long jarg1,
                                               HybridRNA jarg1_,
                                               long jarg2,
                                               ProgressHandler jarg2_)

HybridRNA_StopProgress

public static final void HybridRNA_StopProgress(long jarg1,
                                                HybridRNA jarg1_)

HybridRNA_SWIGUpcast

public static final long HybridRNA_SWIGUpcast(long jarg1)

new_CDblVector__SWIG_0

public static final long new_CDblVector__SWIG_0()

new_CDblVector__SWIG_1

public static final long new_CDblVector__SWIG_1(long jarg1)

new_CIntVector__SWIG_0

public static final long new_CIntVector__SWIG_0()

new_CIntVector__SWIG_1

public static final long new_CIntVector__SWIG_1(long jarg1)

new_datatable

public static final long new_datatable()

new_Dynalign_object__SWIG_0

public static final long new_Dynalign_object__SWIG_0()

new_Dynalign_object__SWIG_1

public static final long new_Dynalign_object__SWIG_1(java.lang.String jarg1,
                                                     java.lang.String jarg2,
                                                     boolean jarg3)

new_Dynalign_object__SWIG_2

public static final long new_Dynalign_object__SWIG_2(java.lang.String jarg1,
                                                     java.lang.String jarg2)

new_Dynalign_object__SWIG_3

public static final long new_Dynalign_object__SWIG_3(java.lang.String jarg1,
                                                     int jarg2,
                                                     java.lang.String jarg3,
                                                     int jarg4,
                                                     boolean jarg5)

new_Dynalign_object__SWIG_4

public static final long new_Dynalign_object__SWIG_4(java.lang.String jarg1,
                                                     int jarg2,
                                                     java.lang.String jarg3,
                                                     int jarg4)

new_Dynalign_object__SWIG_5

public static final long new_Dynalign_object__SWIG_5(java.lang.String jarg1,
                                                     int jarg2,
                                                     java.lang.String jarg3,
                                                     int jarg4,
                                                     long jarg5,
                                                     Thermodynamics jarg5_)

new_Dynalign_object__SWIG_6

public static final long new_Dynalign_object__SWIG_6(java.lang.String jarg1)

new_Dynalign_object__SWIG_7

public static final long new_Dynalign_object__SWIG_7(java.lang.String jarg1,
                                                     short jarg2,
                                                     short jarg3,
                                                     short jarg4,
                                                     short jarg5)

new_HybridRNA__SWIG_0

public static final long new_HybridRNA__SWIG_0(java.lang.String jarg1,
                                               java.lang.String jarg2,
                                               boolean jarg3)

new_HybridRNA__SWIG_1

public static final long new_HybridRNA__SWIG_1(java.lang.String jarg1,
                                               java.lang.String jarg2)

new_HybridRNA__SWIG_2

public static final long new_HybridRNA__SWIG_2(java.lang.String jarg1,
                                               int jarg2,
                                               java.lang.String jarg3,
                                               int jarg4,
                                               boolean jarg5)

new_HybridRNA__SWIG_3

public static final long new_HybridRNA__SWIG_3(java.lang.String jarg1,
                                               int jarg2,
                                               java.lang.String jarg3,
                                               int jarg4)

new_HybridRNA__SWIG_4

public static final long new_HybridRNA__SWIG_4(java.lang.String jarg1,
                                               int jarg2,
                                               java.lang.String jarg3,
                                               int jarg4,
                                               java.lang.String jarg5)

new_PartialProgress

public static final long new_PartialProgress(long jarg1,
                                             ProgressHandler jarg1_)

new_RNA__SWIG_0

public static final long new_RNA__SWIG_0(java.lang.String jarg1,
                                         boolean jarg2)

new_RNA__SWIG_1

public static final long new_RNA__SWIG_1(java.lang.String jarg1)

new_RNA__SWIG_2

public static final long new_RNA__SWIG_2(java.lang.String jarg1,
                                         int jarg2,
                                         java.lang.String jarg3,
                                         boolean jarg4,
                                         boolean jarg5)

new_RNA__SWIG_3

public static final long new_RNA__SWIG_3(java.lang.String jarg1,
                                         int jarg2,
                                         java.lang.String jarg3,
                                         boolean jarg4)

new_RNA__SWIG_4

public static final long new_RNA__SWIG_4(java.lang.String jarg1,
                                         int jarg2,
                                         java.lang.String jarg3)

new_RNA__SWIG_5

public static final long new_RNA__SWIG_5(java.lang.String jarg1,
                                         int jarg2,
                                         long jarg3,
                                         Thermodynamics jarg3_)

new_RNA__SWIG_6

public static final long new_RNA__SWIG_6(java.lang.String jarg1,
                                         int jarg2,
                                         boolean jarg3)

new_RNA__SWIG_7

public static final long new_RNA__SWIG_7(java.lang.String jarg1,
                                         int jarg2)

new_RNA__SWIG_8

public static final long new_RNA__SWIG_8(boolean jarg1)

new_RNA__SWIG_9

public static final long new_RNA__SWIG_9()

new_SimpleProgressHandler

public static final long new_SimpleProgressHandler()

new_singlestructure

public static final long new_singlestructure(int jarg1)

new_structure__SWIG_0

public static final long new_structure__SWIG_0(int jarg1)

new_structure__SWIG_1

public static final long new_structure__SWIG_1()

new_Thermodynamics__SWIG_0

public static final long new_Thermodynamics__SWIG_0(boolean jarg1,
                                                    java.lang.String jarg2,
                                                    double jarg3)

new_Thermodynamics__SWIG_1

public static final long new_Thermodynamics__SWIG_1(boolean jarg1,
                                                    java.lang.String jarg2)

new_Thermodynamics__SWIG_2

public static final long new_Thermodynamics__SWIG_2(boolean jarg1)

new_Thermodynamics__SWIG_3

public static final long new_Thermodynamics__SWIG_3()

new_Thermodynamics__SWIG_4

public static final long new_Thermodynamics__SWIG_4(long jarg1,
                                                    Thermodynamics jarg1_)

new_TProgressDialog

public static final long new_TProgressDialog()

new_TwoRNA__SWIG_0

public static final long new_TwoRNA__SWIG_0(java.lang.String jarg1,
                                            java.lang.String jarg2,
                                            boolean jarg3)

new_TwoRNA__SWIG_1

public static final long new_TwoRNA__SWIG_1(java.lang.String jarg1,
                                            java.lang.String jarg2)

new_TwoRNA__SWIG_2

public static final long new_TwoRNA__SWIG_2(java.lang.String jarg1,
                                            int jarg2,
                                            java.lang.String jarg3,
                                            int jarg4,
                                            boolean jarg5)

new_TwoRNA__SWIG_3

public static final long new_TwoRNA__SWIG_3(java.lang.String jarg1,
                                            int jarg2,
                                            java.lang.String jarg3,
                                            int jarg4)

new_TwoRNA__SWIG_4

public static final long new_TwoRNA__SWIG_4(java.lang.String jarg1,
                                            int jarg2,
                                            java.lang.String jarg3,
                                            int jarg4,
                                            long jarg5,
                                            Thermodynamics jarg5_)

new_TwoRNA__SWIG_5

public static final long new_TwoRNA__SWIG_5()

PartialProgress_advanceToNextStep

public static final void PartialProgress_advanceToNextStep(long jarg1,
                                                           PartialProgress jarg1_,
                                                           int jarg2)

PartialProgress_cancel

public static final void PartialProgress_cancel(long jarg1,
                                                PartialProgress jarg1_)

PartialProgress_canceled

public static final boolean PartialProgress_canceled(long jarg1,
                                                     PartialProgress jarg1_)

PartialProgress_setClient

public static final void PartialProgress_setClient(long jarg1,
                                                   PartialProgress jarg1_,
                                                   long jarg2,
                                                   ProgressHandler jarg2_)

PartialProgress_setNextStep

public static final void PartialProgress_setNextStep(long jarg1,
                                                     PartialProgress jarg1_,
                                                     int jarg2)

PartialProgress_setWorkComplete

public static final void PartialProgress_setWorkComplete(long jarg1,
                                                         PartialProgress jarg1_,
                                                         int jarg2)

PartialProgress_stepComplete

public static final void PartialProgress_stepComplete(long jarg1,
                                                      PartialProgress jarg1_)

PartialProgress_SWIGUpcast

public static final long PartialProgress_SWIGUpcast(long jarg1)

PartialProgress_update

public static final void PartialProgress_update(long jarg1,
                                                PartialProgress jarg1_,
                                                int jarg2)

PartialProgress_workInNextStep_get

public static final int PartialProgress_workInNextStep_get(long jarg1,
                                                           PartialProgress jarg1_)

PartialProgress_workInNextStep_set

public static final void PartialProgress_workInNextStep_set(long jarg1,
                                                            PartialProgress jarg1_,
                                                            int jarg2)

ProgressHandler_cancel

public static final void ProgressHandler_cancel(long jarg1,
                                                ProgressHandler jarg1_)

ProgressHandler_canceled

public static final boolean ProgressHandler_canceled(long jarg1,
                                                     ProgressHandler jarg1_)

ProgressHandler_progress

public static final int ProgressHandler_progress(long jarg1,
                                                 ProgressHandler jarg1_)

ProgressHandler_reset

public static final void ProgressHandler_reset(long jarg1,
                                               ProgressHandler jarg1_)

ProgressHandler_update__SWIG_0

public static final void ProgressHandler_update__SWIG_0(long jarg1,
                                                        ProgressHandler jarg1_,
                                                        int jarg2)

ProgressHandler_update__SWIG_1

public static final void ProgressHandler_update__SWIG_1(long jarg1,
                                                        ProgressHandler jarg1_,
                                                        double jarg2,
                                                        double jarg3)

ProgressHandler_updateFraction

public static final void ProgressHandler_updateFraction(long jarg1,
                                                        ProgressHandler jarg1_,
                                                        double jarg2)

RNA_AddComment__SWIG_0

public static final int RNA_AddComment__SWIG_0(long jarg1,
                                               RNA jarg1_,
                                               java.lang.String jarg2,
                                               int jarg3)

RNA_AddComment__SWIG_1

public static final int RNA_AddComment__SWIG_1(long jarg1,
                                               RNA jarg1_,
                                               java.lang.String jarg2)

RNA_BreakPseudoknot__SWIG_0

public static final int RNA_BreakPseudoknot__SWIG_0(long jarg1,
                                                    RNA jarg1_,
                                                    boolean jarg2,
                                                    int jarg3,
                                                    boolean jarg4)

RNA_BreakPseudoknot__SWIG_1

public static final int RNA_BreakPseudoknot__SWIG_1(long jarg1,
                                                    RNA jarg1_,
                                                    boolean jarg2,
                                                    int jarg3)

RNA_BreakPseudoknot__SWIG_2

public static final int RNA_BreakPseudoknot__SWIG_2(long jarg1,
                                                    RNA jarg1_,
                                                    boolean jarg2)

RNA_BreakPseudoknot__SWIG_3

public static final int RNA_BreakPseudoknot__SWIG_3(long jarg1,
                                                    RNA jarg1_)

RNA_CalculateFreeEnergy__SWIG_0

public static final double RNA_CalculateFreeEnergy__SWIG_0(long jarg1,
                                                           RNA jarg1_,
                                                           int jarg2,
                                                           boolean jarg3)

RNA_CalculateFreeEnergy__SWIG_1

public static final double RNA_CalculateFreeEnergy__SWIG_1(long jarg1,
                                                           RNA jarg1_,
                                                           int jarg2)

RNA_CalculateFreeEnergy__SWIG_2

public static final double RNA_CalculateFreeEnergy__SWIG_2(long jarg1,
                                                           RNA jarg1_)

RNA_ContainsPseudoknot

public static final boolean RNA_ContainsPseudoknot(long jarg1,
                                                   RNA jarg1_,
                                                   int jarg2)

RNA_CopyThermo

public static final void RNA_CopyThermo(long jarg1,
                                        RNA jarg1_,
                                        long jarg2,
                                        Thermodynamics jarg2_)

RNA_DetermineDrawingCoordinates__SWIG_0

public static final int RNA_DetermineDrawingCoordinates__SWIG_0(long jarg1,
                                                                RNA jarg1_,
                                                                int jarg2,
                                                                int jarg3,
                                                                int jarg4)

RNA_DetermineDrawingCoordinates__SWIG_1

public static final int RNA_DetermineDrawingCoordinates__SWIG_1(long jarg1,
                                                                RNA jarg1_,
                                                                int jarg2,
                                                                int jarg3)

RNA_EnsureStructureCapcacity

public static final void RNA_EnsureStructureCapcacity(long jarg1,
                                                      RNA jarg1_,
                                                      int jarg2)

RNA_FoldSingleStrand__SWIG_0

public static final int RNA_FoldSingleStrand__SWIG_0(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     java.lang.String jarg5,
                                                     int jarg6,
                                                     boolean jarg7,
                                                     boolean jarg8,
                                                     boolean jarg9)

RNA_FoldSingleStrand__SWIG_1

public static final int RNA_FoldSingleStrand__SWIG_1(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     java.lang.String jarg5,
                                                     int jarg6,
                                                     boolean jarg7,
                                                     boolean jarg8)

RNA_FoldSingleStrand__SWIG_2

public static final int RNA_FoldSingleStrand__SWIG_2(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     java.lang.String jarg5,
                                                     int jarg6,
                                                     boolean jarg7)

RNA_FoldSingleStrand__SWIG_3

public static final int RNA_FoldSingleStrand__SWIG_3(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     java.lang.String jarg5,
                                                     int jarg6)

RNA_FoldSingleStrand__SWIG_4

public static final int RNA_FoldSingleStrand__SWIG_4(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4,
                                                     java.lang.String jarg5)

RNA_FoldSingleStrand__SWIG_5

public static final int RNA_FoldSingleStrand__SWIG_5(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3,
                                                     int jarg4)

RNA_FoldSingleStrand__SWIG_6

public static final int RNA_FoldSingleStrand__SWIG_6(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2,
                                                     int jarg3)

RNA_FoldSingleStrand__SWIG_7

public static final int RNA_FoldSingleStrand__SWIG_7(long jarg1,
                                                     RNA jarg1_,
                                                     float jarg2)

RNA_FoldSingleStrand__SWIG_8

public static final int RNA_FoldSingleStrand__SWIG_8(long jarg1,
                                                     RNA jarg1_)

RNA_ForceDoubleStranded

public static final int RNA_ForceDoubleStranded(long jarg1,
                                                RNA jarg1_,
                                                int jarg2)

RNA_ForceFMNCleavage

public static final int RNA_ForceFMNCleavage(long jarg1,
                                             RNA jarg1_,
                                             int jarg2)

RNA_ForceMaximumPairingDistance

public static final int RNA_ForceMaximumPairingDistance(long jarg1,
                                                        RNA jarg1_,
                                                        int jarg2)

RNA_ForceModification

public static final int RNA_ForceModification(long jarg1,
                                              RNA jarg1_,
                                              int jarg2)

RNA_ForcePair

public static final int RNA_ForcePair(long jarg1,
                                      RNA jarg1_,
                                      int jarg2,
                                      int jarg3)

RNA_ForceProhibitPair

public static final int RNA_ForceProhibitPair(long jarg1,
                                              RNA jarg1_,
                                              int jarg2,
                                              int jarg3)

RNA_ForceSingleStranded

public static final int RNA_ForceSingleStranded(long jarg1,
                                                RNA jarg1_,
                                                int jarg2)

RNA_GenerateAllSuboptimalStructures__SWIG_0

public static final int RNA_GenerateAllSuboptimalStructures__SWIG_0(long jarg1,
                                                                    RNA jarg1_,
                                                                    float jarg2,
                                                                    double jarg3)

RNA_GenerateAllSuboptimalStructures__SWIG_1

public static final int RNA_GenerateAllSuboptimalStructures__SWIG_1(long jarg1,
                                                                    RNA jarg1_,
                                                                    float jarg2)

RNA_GenerateAllSuboptimalStructures__SWIG_2

public static final int RNA_GenerateAllSuboptimalStructures__SWIG_2(long jarg1,
                                                                    RNA jarg1_)

RNA_GetBackboneType

public static final boolean RNA_GetBackboneType(long jarg1,
                                                RNA jarg1_)

RNA_GetCommentString__SWIG_0

public static final java.lang.String RNA_GetCommentString__SWIG_0(long jarg1,
                                                                  RNA jarg1_,
                                                                  int jarg2)

RNA_GetCommentString__SWIG_1

public static final java.lang.String RNA_GetCommentString__SWIG_1(long jarg1,
                                                                  RNA jarg1_)

RNA_GetEnsembleDefect__SWIG_0

public static final double RNA_GetEnsembleDefect__SWIG_0(long jarg1,
                                                         RNA jarg1_,
                                                         int jarg2)

RNA_GetEnsembleDefect__SWIG_1

public static final double RNA_GetEnsembleDefect__SWIG_1(long jarg1,
                                                         RNA jarg1_)

RNA_GetEnsembleEnergy

public static final double RNA_GetEnsembleEnergy(long jarg1,
                                                 RNA jarg1_)

RNA_GetErrorCode

public static final int RNA_GetErrorCode(long jarg1,
                                         RNA jarg1_)

RNA_GetErrorDetails

public static final java.lang.String RNA_GetErrorDetails(long jarg1,
                                                         RNA jarg1_)

RNA_GetErrorMessage

public static final java.lang.String RNA_GetErrorMessage(int jarg1)

RNA_GetForcedDoubleStranded

public static final int RNA_GetForcedDoubleStranded(long jarg1,
                                                    RNA jarg1_,
                                                    int jarg2)

RNA_GetForcedFMNCleavage

public static final int RNA_GetForcedFMNCleavage(long jarg1,
                                                 RNA jarg1_,
                                                 int jarg2)

RNA_GetForcedModification

public static final int RNA_GetForcedModification(long jarg1,
                                                  RNA jarg1_,
                                                  int jarg2)

RNA_GetForcedPair

public static final int RNA_GetForcedPair(long jarg1,
                                          RNA jarg1_,
                                          int jarg2,
                                          boolean jarg3)

RNA_GetForcedProhibitedPair

public static final int RNA_GetForcedProhibitedPair(long jarg1,
                                                    RNA jarg1_,
                                                    int jarg2,
                                                    boolean jarg3)

RNA_GetForcedSingleStranded

public static final int RNA_GetForcedSingleStranded(long jarg1,
                                                    RNA jarg1_,
                                                    int jarg2)

RNA_GetFreeEnergy

public static final double RNA_GetFreeEnergy(long jarg1,
                                             RNA jarg1_,
                                             int jarg2)

RNA_GetFullErrorMessage

public static final java.lang.String RNA_GetFullErrorMessage(long jarg1,
                                                             RNA jarg1_)

RNA_getIntAt

public static final int RNA_getIntAt(long jarg1,
                                     RNA jarg1_,
                                     int jarg2)

RNA_getInts

public static final int RNA_getInts(long jarg1,
                                    RNA jarg1_,
                                    int[] jarg2,
                                    int jarg3)

RNA_GetLabelXCoordinate

public static final int RNA_GetLabelXCoordinate(long jarg1,
                                                RNA jarg1_,
                                                int jarg2)

RNA_GetLabelYCoordinate

public static final int RNA_GetLabelYCoordinate(long jarg1,
                                                RNA jarg1_,
                                                int jarg2)

RNA_GetMaximumPairingDistance

public static final int RNA_GetMaximumPairingDistance(long jarg1,
                                                      RNA jarg1_)

RNA_GetNucleotide

public static final char RNA_GetNucleotide(long jarg1,
                                           RNA jarg1_,
                                           int jarg2)

RNA_GetNucleotideXCoordinate

public static final int RNA_GetNucleotideXCoordinate(long jarg1,
                                                     RNA jarg1_,
                                                     int jarg2)

RNA_GetNucleotideYCoordinate

public static final int RNA_GetNucleotideYCoordinate(long jarg1,
                                                     RNA jarg1_,
                                                     int jarg2)

RNA_GetNumberOfForcedDoubleStranded

public static final int RNA_GetNumberOfForcedDoubleStranded(long jarg1,
                                                            RNA jarg1_)

RNA_GetNumberOfForcedFMNCleavages

public static final int RNA_GetNumberOfForcedFMNCleavages(long jarg1,
                                                          RNA jarg1_)

RNA_GetNumberOfForcedModifications

public static final int RNA_GetNumberOfForcedModifications(long jarg1,
                                                           RNA jarg1_)

RNA_GetNumberOfForcedPairs

public static final int RNA_GetNumberOfForcedPairs(long jarg1,
                                                   RNA jarg1_)

RNA_GetNumberOfForcedProhibitedPairs

public static final int RNA_GetNumberOfForcedProhibitedPairs(long jarg1,
                                                             RNA jarg1_)

RNA_GetNumberOfForcedSingleStranded

public static final int RNA_GetNumberOfForcedSingleStranded(long jarg1,
                                                            RNA jarg1_)

RNA_GetPair__SWIG_0

public static final int RNA_GetPair__SWIG_0(long jarg1,
                                            RNA jarg1_,
                                            int jarg2,
                                            int jarg3)

RNA_GetPair__SWIG_1

public static final int RNA_GetPair__SWIG_1(long jarg1,
                                            RNA jarg1_,
                                            int jarg2)

RNA_GetPairEnergy

public static final double RNA_GetPairEnergy(long jarg1,
                                             RNA jarg1_,
                                             int jarg2,
                                             int jarg3)

RNA_GetPairProbabilities

public static final int RNA_GetPairProbabilities(long jarg1,
                                                 RNA jarg1_,
                                                 double[] jarg2,
                                                 int jarg3)

RNA_GetPairProbability

public static final double RNA_GetPairProbability(long jarg1,
                                                  RNA jarg1_,
                                                  int jarg2,
                                                  int jarg3)

RNA_GetProgress

public static final long RNA_GetProgress(long jarg1,
                                         RNA jarg1_)

RNA_GetSequence

public static final java.lang.String RNA_GetSequence(long jarg1,
                                                     RNA jarg1_)

RNA_GetSequenceLength

public static final int RNA_GetSequenceLength(long jarg1,
                                              RNA jarg1_)

RNA_GetStructure

public static final long RNA_GetStructure(long jarg1,
                                          RNA jarg1_)

RNA_GetStructureNumber

public static final int RNA_GetStructureNumber(long jarg1,
                                               RNA jarg1_)

RNA_initInts

public static final void RNA_initInts(long jarg1,
                                      RNA jarg1_)

RNA_MaximizeExpectedAccuracy__SWIG_0

public static final int RNA_MaximizeExpectedAccuracy__SWIG_0(long jarg1,
                                                             RNA jarg1_,
                                                             double jarg2,
                                                             int jarg3,
                                                             int jarg4,
                                                             double jarg5)

RNA_MaximizeExpectedAccuracy__SWIG_1

public static final int RNA_MaximizeExpectedAccuracy__SWIG_1(long jarg1,
                                                             RNA jarg1_,
                                                             double jarg2,
                                                             int jarg3,
                                                             int jarg4)

RNA_MaximizeExpectedAccuracy__SWIG_2

public static final int RNA_MaximizeExpectedAccuracy__SWIG_2(long jarg1,
                                                             RNA jarg1_,
                                                             double jarg2,
                                                             int jarg3)

RNA_MaximizeExpectedAccuracy__SWIG_3

public static final int RNA_MaximizeExpectedAccuracy__SWIG_3(long jarg1,
                                                             RNA jarg1_,
                                                             double jarg2)

RNA_MaximizeExpectedAccuracy__SWIG_4

public static final int RNA_MaximizeExpectedAccuracy__SWIG_4(long jarg1,
                                                             RNA jarg1_)

RNA_PartitionFunction__SWIG_0

public static final int RNA_PartitionFunction__SWIG_0(long jarg1,
                                                      RNA jarg1_,
                                                      java.lang.String jarg2,
                                                      double jarg3,
                                                      boolean jarg4,
                                                      boolean jarg5)

RNA_PartitionFunction__SWIG_1

public static final int RNA_PartitionFunction__SWIG_1(long jarg1,
                                                      RNA jarg1_,
                                                      java.lang.String jarg2,
                                                      double jarg3,
                                                      boolean jarg4)

RNA_PartitionFunction__SWIG_2

public static final int RNA_PartitionFunction__SWIG_2(long jarg1,
                                                      RNA jarg1_,
                                                      java.lang.String jarg2,
                                                      double jarg3)

RNA_PartitionFunction__SWIG_3

public static final int RNA_PartitionFunction__SWIG_3(long jarg1,
                                                      RNA jarg1_,
                                                      java.lang.String jarg2)

RNA_PartitionFunction__SWIG_4

public static final int RNA_PartitionFunction__SWIG_4(long jarg1,
                                                      RNA jarg1_)

RNA_PredictProbablePairs__SWIG_0

public static final int RNA_PredictProbablePairs__SWIG_0(long jarg1,
                                                         RNA jarg1_,
                                                         float jarg2)

RNA_PredictProbablePairs__SWIG_1

public static final int RNA_PredictProbablePairs__SWIG_1(long jarg1,
                                                         RNA jarg1_)

RNA_ProbKnot__SWIG_0

public static final int RNA_ProbKnot__SWIG_0(long jarg1,
                                             RNA jarg1_,
                                             int jarg2,
                                             int jarg3)

RNA_ProbKnot__SWIG_1

public static final int RNA_ProbKnot__SWIG_1(long jarg1,
                                             RNA jarg1_,
                                             int jarg2)

RNA_ProbKnot__SWIG_2

public static final int RNA_ProbKnot__SWIG_2(long jarg1,
                                             RNA jarg1_)

RNA_ProbKnotFromSample__SWIG_0

public static final int RNA_ProbKnotFromSample__SWIG_0(long jarg1,
                                                       RNA jarg1_,
                                                       int jarg2,
                                                       int jarg3)

RNA_ProbKnotFromSample__SWIG_1

public static final int RNA_ProbKnotFromSample__SWIG_1(long jarg1,
                                                       RNA jarg1_,
                                                       int jarg2)

RNA_ProbKnotFromSample__SWIG_2

public static final int RNA_ProbKnotFromSample__SWIG_2(long jarg1,
                                                       RNA jarg1_)

RNA_ReadConstraints

public static final int RNA_ReadConstraints(long jarg1,
                                            RNA jarg1_,
                                            java.lang.String jarg2)

RNA_ReadDMS

public static final int RNA_ReadDMS(long jarg1,
                                    RNA jarg1_,
                                    java.lang.String jarg2)

RNA_ReadDSO

public static final int RNA_ReadDSO(long jarg1,
                                    RNA jarg1_,
                                    java.lang.String jarg2)

RNA_ReadExperimentalPairBonus

public static final int RNA_ReadExperimentalPairBonus(long jarg1,
                                                      RNA jarg1_,
                                                      java.lang.String jarg2,
                                                      double jarg3,
                                                      double jarg4)

RNA_ReadSHAPE__SWIG_0

public static final int RNA_ReadSHAPE__SWIG_0(long jarg1,
                                              RNA jarg1_,
                                              java.lang.String jarg2,
                                              double jarg3,
                                              double jarg4,
                                              int jarg5,
                                              boolean jarg6)

RNA_ReadSHAPE__SWIG_1

public static final int RNA_ReadSHAPE__SWIG_1(long jarg1,
                                              RNA jarg1_,
                                              java.lang.String jarg2,
                                              double jarg3,
                                              double jarg4,
                                              int jarg5)

RNA_ReadSHAPE__SWIG_2

public static final int RNA_ReadSHAPE__SWIG_2(long jarg1,
                                              RNA jarg1_,
                                              java.lang.String jarg2,
                                              double jarg3,
                                              double jarg4)

RNA_ReadSHAPE__SWIG_3

public static final int RNA_ReadSHAPE__SWIG_3(long jarg1,
                                              RNA jarg1_,
                                              java.lang.String jarg2,
                                              double jarg3,
                                              double jarg4,
                                              double jarg5,
                                              double jarg6,
                                              int jarg7)

RNA_ReadSHAPE__SWIG_4

public static final int RNA_ReadSHAPE__SWIG_4(long jarg1,
                                              RNA jarg1_,
                                              java.lang.String jarg2,
                                              double jarg3,
                                              double jarg4,
                                              double jarg5,
                                              double jarg6)

RNA_ReadSSO

public static final int RNA_ReadSSO(long jarg1,
                                    RNA jarg1_,
                                    java.lang.String jarg2)

RNA_ReFoldSingleStrand__SWIG_0

public static final int RNA_ReFoldSingleStrand__SWIG_0(long jarg1,
                                                       RNA jarg1_,
                                                       float jarg2,
                                                       int jarg3,
                                                       int jarg4)

RNA_ReFoldSingleStrand__SWIG_1

public static final int RNA_ReFoldSingleStrand__SWIG_1(long jarg1,
                                                       RNA jarg1_,
                                                       float jarg2,
                                                       int jarg3)

RNA_ReFoldSingleStrand__SWIG_2

public static final int RNA_ReFoldSingleStrand__SWIG_2(long jarg1,
                                                       RNA jarg1_,
                                                       float jarg2)

RNA_ReFoldSingleStrand__SWIG_3

public static final int RNA_ReFoldSingleStrand__SWIG_3(long jarg1,
                                                       RNA jarg1_)

RNA_RemoveBasePair__SWIG_0

public static final int RNA_RemoveBasePair__SWIG_0(long jarg1,
                                                   RNA jarg1_,
                                                   int jarg2,
                                                   int jarg3)

RNA_RemoveBasePair__SWIG_1

public static final int RNA_RemoveBasePair__SWIG_1(long jarg1,
                                                   RNA jarg1_,
                                                   int jarg2)

RNA_RemoveConstraints

public static final void RNA_RemoveConstraints(long jarg1,
                                               RNA jarg1_)

RNA_RemovePairs__SWIG_0

public static final int RNA_RemovePairs__SWIG_0(long jarg1,
                                                RNA jarg1_,
                                                int jarg2,
                                                boolean jarg3)

RNA_RemovePairs__SWIG_1

public static final int RNA_RemovePairs__SWIG_1(long jarg1,
                                                RNA jarg1_,
                                                int jarg2)

RNA_RemovePairs__SWIG_2

public static final int RNA_RemovePairs__SWIG_2(long jarg1,
                                                RNA jarg1_)

RNA_ResetError

public static final void RNA_ResetError(long jarg1,
                                        RNA jarg1_)

RNA_SetErrorDetails

public static final void RNA_SetErrorDetails(long jarg1,
                                             RNA jarg1_,
                                             java.lang.String jarg2)

RNA_SetExtrinsic

public static final int RNA_SetExtrinsic(long jarg1,
                                         RNA jarg1_,
                                         int jarg2,
                                         int jarg3,
                                         double jarg4)

RNA_SetProgress

public static final void RNA_SetProgress(long jarg1,
                                         RNA jarg1_,
                                         long jarg2,
                                         ProgressHandler jarg2_)

RNA_SpecifyPair__SWIG_0

public static final int RNA_SpecifyPair__SWIG_0(long jarg1,
                                                RNA jarg1_,
                                                int jarg2,
                                                int jarg3,
                                                int jarg4)

RNA_SpecifyPair__SWIG_1

public static final int RNA_SpecifyPair__SWIG_1(long jarg1,
                                                RNA jarg1_,
                                                int jarg2,
                                                int jarg3)

RNA_Stochastic__SWIG_0

public static final int RNA_Stochastic__SWIG_0(long jarg1,
                                               RNA jarg1_,
                                               int jarg2,
                                               int jarg3)

RNA_Stochastic__SWIG_1

public static final int RNA_Stochastic__SWIG_1(long jarg1,
                                               RNA jarg1_,
                                               int jarg2)

RNA_Stochastic__SWIG_2

public static final int RNA_Stochastic__SWIG_2(long jarg1,
                                               RNA jarg1_)

RNA_StopProgress

public static final void RNA_StopProgress(long jarg1,
                                          RNA jarg1_)

RNA_SWIGUpcast

public static final long RNA_SWIGUpcast(long jarg1)

RNA_WriteConstraints

public static final int RNA_WriteConstraints(long jarg1,
                                             RNA jarg1_,
                                             java.lang.String jarg2)

RNA_WriteCt

public static final int RNA_WriteCt(long jarg1,
                                    RNA jarg1_,
                                    java.lang.String jarg2)

RNA_WriteDotBracket__SWIG_0

public static final int RNA_WriteDotBracket__SWIG_0(long jarg1,
                                                    RNA jarg1_,
                                                    java.lang.String jarg2,
                                                    int jarg3,
                                                    int jarg4)

RNA_WriteDotBracket__SWIG_1

public static final int RNA_WriteDotBracket__SWIG_1(long jarg1,
                                                    RNA jarg1_,
                                                    java.lang.String jarg2,
                                                    int jarg3)

RNA_WriteDotBracket__SWIG_2

public static final int RNA_WriteDotBracket__SWIG_2(long jarg1,
                                                    RNA jarg1_,
                                                    java.lang.String jarg2)

RNA_WriteThermodynamicDetails__SWIG_0

public static final int RNA_WriteThermodynamicDetails__SWIG_0(long jarg1,
                                                              RNA jarg1_,
                                                              java.lang.String jarg2,
                                                              boolean jarg3)

RNA_WriteThermodynamicDetails__SWIG_1

public static final int RNA_WriteThermodynamicDetails__SWIG_1(long jarg1,
                                                              RNA jarg1_,
                                                              java.lang.String jarg2)

SEQUENCE_STRING_get

public static final int SEQUENCE_STRING_get()

setDataPath

public static final void setDataPath(java.lang.String jarg1)

SimpleProgressHandler_SWIGUpcast

public static final long SimpleProgressHandler_SWIGUpcast(long jarg1)

singlestructure_ctlabel_get

public static final java.lang.String singlestructure_ctlabel_get(long jarg1,
                                                                 singlestructure jarg1_)

singlestructure_ctlabel_set

public static final void singlestructure_ctlabel_set(long jarg1,
                                                     singlestructure jarg1_,
                                                     java.lang.String jarg2)

singlestructure_energy_get

public static final int singlestructure_energy_get(long jarg1,
                                                   singlestructure jarg1_)

singlestructure_energy_set

public static final void singlestructure_energy_set(long jarg1,
                                                    singlestructure jarg1_,
                                                    int jarg2)

singlestructure_getBasePair

public static final int singlestructure_getBasePair(long jarg1,
                                                    singlestructure jarg1_,
                                                    int jarg2)

singlestructure_getSequenceLength

public static final int singlestructure_getSequenceLength(long jarg1,
                                                          singlestructure jarg1_)

singlestructure_setBasePair

public static final void singlestructure_setBasePair(long jarg1,
                                                     singlestructure jarg1_,
                                                     int jarg2,
                                                     int jarg3)

singlestructure_setSequenceLength

public static final void singlestructure_setSequenceLength(long jarg1,
                                                           singlestructure jarg1_,
                                                           int jarg2)

structure_AddDouble

public static final void structure_AddDouble(long jarg1,
                                             structure jarg1_,
                                             int jarg2)

structure_AddForbiddenPair

public static final void structure_AddForbiddenPair(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2,
                                                    int jarg3)

structure_AddGUPair

public static final void structure_AddGUPair(long jarg1,
                                             structure jarg1_,
                                             int jarg2)

structure_AddModified

public static final void structure_AddModified(long jarg1,
                                               structure jarg1_,
                                               int jarg2)

structure_AddPair

public static final void structure_AddPair(long jarg1,
                                           structure jarg1_,
                                           int jarg2,
                                           int jarg3)

structure_AddSingle

public static final void structure_AddSingle(long jarg1,
                                             structure jarg1_,
                                             int jarg2)

structure_AddStructure

public static final void structure_AddStructure(long jarg1,
                                                structure jarg1_)

structure_allocateconstant

public static final void structure_allocateconstant(long jarg1,
                                                    structure jarg1_)

structure_AllocateSHAPE

public static final void structure_AllocateSHAPE(long jarg1,
                                                 structure jarg1_)

structure_allocatetem

public static final void structure_allocatetem(long jarg1,
                                               structure jarg1_)

structure_BreakPseudoknots

public static final void structure_BreakPseudoknots(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2)

structure_CleanStructure

public static final void structure_CleanStructure(long jarg1,
                                                  structure jarg1_,
                                                  int jarg2)

structure_ctout

public static final int structure_ctout(long jarg1,
                                        structure jarg1_,
                                        java.lang.String jarg2)

structure_DeleteSHAPE

public static final void structure_DeleteSHAPE(long jarg1,
                                               structure jarg1_)

structure_DistanceLimited

public static final boolean structure_DistanceLimited(long jarg1,
                                                      structure jarg1_)

structure_FindPseudoknots__SWIG_0

public static final void structure_FindPseudoknots__SWIG_0(long jarg1,
                                                           structure jarg1_,
                                                           int jarg2,
                                                           long jarg3,
                                                           CIntVector jarg3_,
                                                           long jarg4,
                                                           CIntVector jarg4_)

structure_FindPseudoknots__SWIG_1

public static final void structure_FindPseudoknots__SWIG_1(long jarg1,
                                                           structure jarg1_,
                                                           int jarg2,
                                                           long jarg3,
                                                           CIntVector jarg3_)

structure_FindPseudoknots__SWIG_2

public static final void structure_FindPseudoknots__SWIG_2(long jarg1,
                                                           structure jarg1_,
                                                           int jarg2)

structure_GetBase

public static final int structure_GetBase(long jarg1,
                                          structure jarg1_,
                                          int jarg2)

structure_GetCtLabel

public static final java.lang.String structure_GetCtLabel(long jarg1,
                                                          structure jarg1_,
                                                          int jarg2)

structure_GetDouble

public static final int structure_GetDouble(long jarg1,
                                            structure jarg1_,
                                            int jarg2)

structure_GetEnergy

public static final int structure_GetEnergy(long jarg1,
                                            structure jarg1_,
                                            int jarg2)

structure_GetErrorDetails

public static final java.lang.String structure_GetErrorDetails(long jarg1,
                                                               structure jarg1_)

structure_GetForbiddenPair3

public static final int structure_GetForbiddenPair3(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2)

structure_GetForbiddenPair5

public static final int structure_GetForbiddenPair5(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2)

structure_GetGUpair

public static final int structure_GetGUpair(long jarg1,
                                            structure jarg1_,
                                            int jarg2)

structure_GetModified

public static final int structure_GetModified(long jarg1,
                                              structure jarg1_,
                                              int jarg2)

structure_GetNumberofDoubles

public static final int structure_GetNumberofDoubles(long jarg1,
                                                     structure jarg1_)

structure_GetNumberofForbiddenPairs

public static final int structure_GetNumberofForbiddenPairs(long jarg1,
                                                            structure jarg1_)

structure_GetNumberofGU

public static final int structure_GetNumberofGU(long jarg1,
                                                structure jarg1_)

structure_GetNumberofModified

public static final int structure_GetNumberofModified(long jarg1,
                                                      structure jarg1_)

structure_GetNumberofPairs

public static final int structure_GetNumberofPairs(long jarg1,
                                                   structure jarg1_)

structure_GetNumberofSingles

public static final int structure_GetNumberofSingles(long jarg1,
                                                     structure jarg1_)

structure_GetNumberofStructures

public static final int structure_GetNumberofStructures(long jarg1,
                                                        structure jarg1_)

structure_GetPair__SWIG_0

public static final int structure_GetPair__SWIG_0(long jarg1,
                                                  structure jarg1_,
                                                  int jarg2,
                                                  int jarg3)

structure_GetPair__SWIG_1

public static final int structure_GetPair__SWIG_1(long jarg1,
                                                  structure jarg1_,
                                                  int jarg2)

structure_GetPair3

public static final int structure_GetPair3(long jarg1,
                                           structure jarg1_,
                                           int jarg2)

structure_GetPair5

public static final int structure_GetPair5(long jarg1,
                                           structure jarg1_,
                                           int jarg2)

structure_GetPairingDistanceLimit

public static final int structure_GetPairingDistanceLimit(long jarg1,
                                                          structure jarg1_)

structure_GetPseudoknotRanks__SWIG_0

public static final void structure_GetPseudoknotRanks__SWIG_0(long jarg1,
                                                              structure jarg1_,
                                                              long jarg2,
                                                              CIntVector jarg2_,
                                                              int jarg3)

structure_GetPseudoknotRanks__SWIG_1

public static final void structure_GetPseudoknotRanks__SWIG_1(long jarg1,
                                                              structure jarg1_,
                                                              long jarg2,
                                                              CIntVector jarg2_)

structure_GetSequence

public static final java.lang.String structure_GetSequence(long jarg1,
                                                           structure jarg1_)

structure_GetSequenceLabel

public static final java.lang.String structure_GetSequenceLabel(long jarg1,
                                                                structure jarg1_)

structure_GetSequenceLength

public static final int structure_GetSequenceLength(long jarg1,
                                                    structure jarg1_)

structure_GetSingle

public static final int structure_GetSingle(long jarg1,
                                            structure jarg1_,
                                            int jarg2)

structure_GetThermodynamicDataTable

public static final long structure_GetThermodynamicDataTable(long jarg1,
                                                             structure jarg1_)

structure_HasPseudoknots__SWIG_0

public static final boolean structure_HasPseudoknots__SWIG_0(long jarg1,
                                                             structure jarg1_,
                                                             int jarg2)

structure_HasPseudoknots__SWIG_1

public static final boolean structure_HasPseudoknots__SWIG_1(long jarg1,
                                                             structure jarg1_)

structure_IsAlphabetLoaded

public static final boolean structure_IsAlphabetLoaded(long jarg1,
                                                       structure jarg1_)

structure_IsNuc__SWIG_0

public static final boolean structure_IsNuc__SWIG_0(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2,
                                                    char jarg3)

structure_IsNuc__SWIG_1

public static final boolean structure_IsNuc__SWIG_1(long jarg1,
                                                    structure jarg1_,
                                                    int jarg2,
                                                    char jarg3,
                                                    long jarg4,
                                                    datatable jarg4_)

structure_IsThermoDataLoaded

public static final boolean structure_IsThermoDataLoaded(long jarg1,
                                                         structure jarg1_)

structure_kT_get

public static final double structure_kT_get()

structure_openct

public static final int structure_openct(long jarg1,
                                         structure jarg1_,
                                         java.lang.String jarg2)

structure_opendbn

public static final int structure_opendbn(long jarg1,
                                          structure jarg1_,
                                          java.lang.String jarg2)

structure_openseq

public static final int structure_openseq(long jarg1,
                                          structure jarg1_,
                                          java.lang.String jarg2)

structure_openseqx

public static final int structure_openseqx(long jarg1,
                                           structure jarg1_,
                                           java.lang.String jarg2)

structure_ProblemwithStructures

public static final boolean structure_ProblemwithStructures(long jarg1,
                                                            structure jarg1_)

structure_ReadExperimentalPairBonus__SWIG_0

public static final int structure_ReadExperimentalPairBonus__SWIG_0(long jarg1,
                                                                    structure jarg1_,
                                                                    java.lang.String jarg2,
                                                                    double jarg3,
                                                                    double jarg4)

structure_ReadExperimentalPairBonus__SWIG_1

public static final int structure_ReadExperimentalPairBonus__SWIG_1(long jarg1,
                                                                    structure jarg1_,
                                                                    java.lang.String jarg2,
                                                                    double jarg3)

structure_ReadExperimentalPairBonus__SWIG_2

public static final int structure_ReadExperimentalPairBonus__SWIG_2(long jarg1,
                                                                    structure jarg1_,
                                                                    java.lang.String jarg2)

structure_ReadOffset

public static final int structure_ReadOffset(long jarg1,
                                             structure jarg1_,
                                             java.lang.String jarg2,
                                             java.lang.String jarg3)

structure_ReadSHAPE__SWIG_0

public static final int structure_ReadSHAPE__SWIG_0(long jarg1,
                                                    structure jarg1_,
                                                    java.lang.String jarg2,
                                                    float jarg3,
                                                    float jarg4)

structure_ReadSHAPE__SWIG_1

public static final int structure_ReadSHAPE__SWIG_1(long jarg1,
                                                    structure jarg1_,
                                                    java.lang.String jarg2,
                                                    int jarg3,
                                                    boolean jarg4)

structure_ReadSHAPE__SWIG_2

public static final int structure_ReadSHAPE__SWIG_2(long jarg1,
                                                    structure jarg1_,
                                                    java.lang.String jarg2,
                                                    int jarg3)

structure_ReadSHAPE__SWIG_3

public static final int structure_ReadSHAPE__SWIG_3(long jarg1,
                                                    structure jarg1_,
                                                    java.lang.String jarg2)

structure_RemoveAllStructures

public static final void structure_RemoveAllStructures(long jarg1,
                                                       structure jarg1_)

structure_RemoveConstraints

public static final void structure_RemoveConstraints(long jarg1,
                                                     structure jarg1_)

structure_RemoveEnergyLabels__SWIG_0

public static final void structure_RemoveEnergyLabels__SWIG_0(long jarg1,
                                                              structure jarg1_,
                                                              java.lang.String jarg2)

structure_RemoveEnergyLabels__SWIG_1

public static final void structure_RemoveEnergyLabels__SWIG_1(long jarg1,
                                                              structure jarg1_)

structure_RemoveLastStructure

public static final void structure_RemoveLastStructure(long jarg1,
                                                       structure jarg1_)

structure_RemovePair__SWIG_0

public static final void structure_RemovePair__SWIG_0(long jarg1,
                                                      structure jarg1_,
                                                      int jarg2,
                                                      int jarg3)

structure_RemovePair__SWIG_1

public static final void structure_RemovePair__SWIG_1(long jarg1,
                                                      structure jarg1_,
                                                      int jarg2)

structure_RemoveStructure

public static final void structure_RemoveStructure(long jarg1,
                                                   structure jarg1_,
                                                   int jarg2)

structure_SetCtLabel

public static final void structure_SetCtLabel(long jarg1,
                                              structure jarg1_,
                                              java.lang.String jarg2,
                                              int jarg3)

structure_SetEnergy

public static final void structure_SetEnergy(long jarg1,
                                             structure jarg1_,
                                             int jarg2,
                                             int jarg3)

structure_SetPair__SWIG_0

public static final void structure_SetPair__SWIG_0(long jarg1,
                                                   structure jarg1_,
                                                   int jarg2,
                                                   int jarg3,
                                                   int jarg4)

structure_SetPair__SWIG_1

public static final void structure_SetPair__SWIG_1(long jarg1,
                                                   structure jarg1_,
                                                   int jarg2,
                                                   int jarg3)

structure_SetPairingDistance

public static final void structure_SetPairingDistance(long jarg1,
                                                      structure jarg1_,
                                                      int jarg2)

structure_SetSequence

public static final int structure_SetSequence(long jarg1,
                                              structure jarg1_,
                                              java.lang.String jarg2)

structure_SetSequenceLabel

public static final void structure_SetSequenceLabel(long jarg1,
                                                    structure jarg1_,
                                                    java.lang.String jarg2)

structure_SetThermodynamicDataTable

public static final void structure_SetThermodynamicDataTable(long jarg1,
                                                             structure jarg1_,
                                                             long jarg2,
                                                             datatable jarg2_)

structure_SHAPEFileRead_get

public static final boolean structure_SHAPEFileRead_get(long jarg1,
                                                        structure jarg1_)

structure_SHAPEFileRead_set

public static final void structure_SHAPEFileRead_set(long jarg1,
                                                     structure jarg1_,
                                                     boolean jarg2)

structure_ShowWarnings_get

public static final int structure_ShowWarnings_get()

structure_ShowWarnings_set

public static final void structure_ShowWarnings_set(int jarg1)

structure_sort

public static final void structure_sort(long jarg1,
                                        structure jarg1_)

structure_SumShapeRepeats_get

public static final boolean structure_SumShapeRepeats_get()

structure_SumShapeRepeats_set

public static final void structure_SumShapeRepeats_set(boolean jarg1)

structure_writedotbracket__SWIG_0

public static final int structure_writedotbracket__SWIG_0(long jarg1,
                                                          structure jarg1_,
                                                          java.lang.String jarg2,
                                                          int jarg3,
                                                          int jarg4)

structure_writedotbracket__SWIG_1

public static final int structure_writedotbracket__SWIG_1(long jarg1,
                                                          structure jarg1_,
                                                          java.lang.String jarg2,
                                                          int jarg3)

structure_writedotbracket__SWIG_2

public static final int structure_writedotbracket__SWIG_2(long jarg1,
                                                          structure jarg1_,
                                                          java.lang.String jarg2)

structure_writeseq__SWIG_0

public static final int structure_writeseq__SWIG_0(long jarg1,
                                                   structure jarg1_,
                                                   java.lang.String jarg2,
                                                   int jarg3,
                                                   boolean jarg4)

structure_writeseq__SWIG_1

public static final int structure_writeseq__SWIG_1(long jarg1,
                                                   structure jarg1_,
                                                   java.lang.String jarg2,
                                                   int jarg3)

structure_writeseq__SWIG_2

public static final int structure_writeseq__SWIG_2(long jarg1,
                                                   structure jarg1_,
                                                   java.lang.String jarg2)

structure_WriteSHAPE__SWIG_0

public static final int structure_WriteSHAPE__SWIG_0(long jarg1,
                                                     structure jarg1_,
                                                     java.lang.String jarg2,
                                                     boolean jarg3)

structure_WriteSHAPE__SWIG_1

public static final int structure_WriteSHAPE__SWIG_1(long jarg1,
                                                     structure jarg1_,
                                                     java.lang.String jarg2)

Thermodynamics_ClearEnergies

public static final void Thermodynamics_ClearEnergies(long jarg1,
                                                      Thermodynamics jarg1_)

Thermodynamics_ClearEnthalpies

public static final void Thermodynamics_ClearEnthalpies(long jarg1,
                                                        Thermodynamics jarg1_)

Thermodynamics_GetAlphabetName

public static final java.lang.String Thermodynamics_GetAlphabetName(long jarg1,
                                                                    Thermodynamics jarg1_)

Thermodynamics_GetDatatable

public static final long Thermodynamics_GetDatatable(long jarg1,
                                                     Thermodynamics jarg1_)

Thermodynamics_GetEnergyRead

public static final boolean Thermodynamics_GetEnergyRead(long jarg1,
                                                         Thermodynamics jarg1_)

Thermodynamics_GetEnthalpyTable__SWIG_0

public static final long Thermodynamics_GetEnthalpyTable__SWIG_0(long jarg1,
                                                                 Thermodynamics jarg1_,
                                                                 java.lang.String jarg2)

Thermodynamics_GetEnthalpyTable__SWIG_1

public static final long Thermodynamics_GetEnthalpyTable__SWIG_1(long jarg1,
                                                                 Thermodynamics jarg1_)

Thermodynamics_GetTemperature

public static final double Thermodynamics_GetTemperature(long jarg1,
                                                         Thermodynamics jarg1_)

Thermodynamics_IsAlphabetRead

public static final boolean Thermodynamics_IsAlphabetRead(long jarg1,
                                                          Thermodynamics jarg1_)

Thermodynamics_isrna_get

public static final boolean Thermodynamics_isrna_get(long jarg1,
                                                     Thermodynamics jarg1_)

Thermodynamics_isrna_set

public static final void Thermodynamics_isrna_set(long jarg1,
                                                  Thermodynamics jarg1_,
                                                  boolean jarg2)

Thermodynamics_ReadThermodynamic__SWIG_0

public static final int Thermodynamics_ReadThermodynamic__SWIG_0(long jarg1,
                                                                 Thermodynamics jarg1_,
                                                                 java.lang.String jarg2,
                                                                 java.lang.String jarg3,
                                                                 double jarg4)

Thermodynamics_ReadThermodynamic__SWIG_1

public static final int Thermodynamics_ReadThermodynamic__SWIG_1(long jarg1,
                                                                 Thermodynamics jarg1_,
                                                                 java.lang.String jarg2,
                                                                 java.lang.String jarg3)

Thermodynamics_ReadThermodynamic__SWIG_2

public static final int Thermodynamics_ReadThermodynamic__SWIG_2(long jarg1,
                                                                 Thermodynamics jarg1_,
                                                                 java.lang.String jarg2)

Thermodynamics_ReadThermodynamic__SWIG_3

public static final int Thermodynamics_ReadThermodynamic__SWIG_3(long jarg1,
                                                                 Thermodynamics jarg1_)

Thermodynamics_ReloadDataTables__SWIG_0

public static final int Thermodynamics_ReloadDataTables__SWIG_0(long jarg1,
                                                                Thermodynamics jarg1_,
                                                                double jarg2)

Thermodynamics_ReloadDataTables__SWIG_1

public static final int Thermodynamics_ReloadDataTables__SWIG_1(long jarg1,
                                                                Thermodynamics jarg1_)

Thermodynamics_SetTemperature

public static final int Thermodynamics_SetTemperature(long jarg1,
                                                      Thermodynamics jarg1_,
                                                      double jarg2)

Thermodynamics_VerifyThermodynamic

public static final boolean Thermodynamics_VerifyThermodynamic(long jarg1,
                                                               Thermodynamics jarg1_)

TProgressDialog_SWIGUpcast

public static final long TProgressDialog_SWIGUpcast(long jarg1)

TProgressDialog_update

public static final void TProgressDialog_update(long jarg1,
                                                TProgressDialog jarg1_,
                                                int jarg2)

TwoRNA_compoundmessage_get

public static final java.lang.String TwoRNA_compoundmessage_get(long jarg1,
                                                                TwoRNA jarg1_)

TwoRNA_compoundmessage_set

public static final void TwoRNA_compoundmessage_set(long jarg1,
                                                    TwoRNA jarg1_,
                                                    java.lang.String jarg2)

TwoRNA_GetErrorCode

public static final int TwoRNA_GetErrorCode(long jarg1,
                                            TwoRNA jarg1_)

TwoRNA_GetErrorDetails

public static final java.lang.String TwoRNA_GetErrorDetails(long jarg1,
                                                            TwoRNA jarg1_)

TwoRNA_GetErrorMessage

public static final java.lang.String TwoRNA_GetErrorMessage(long jarg1,
                                                            TwoRNA jarg1_,
                                                            int jarg2)

TwoRNA_GetErrorMessageString

public static final java.lang.String TwoRNA_GetErrorMessageString(long jarg1,
                                                                  TwoRNA jarg1_,
                                                                  int jarg2)

TwoRNA_GetRNA1

public static final long TwoRNA_GetRNA1(long jarg1,
                                        TwoRNA jarg1_)

TwoRNA_GetRNA2

public static final long TwoRNA_GetRNA2(long jarg1,
                                        TwoRNA jarg1_)

TwoRNA_GetTemperature

public static final double TwoRNA_GetTemperature(long jarg1,
                                                 TwoRNA jarg1_)

TwoRNA_ResetError

public static final void TwoRNA_ResetError(long jarg1,
                                           TwoRNA jarg1_)

TwoRNA_SetErrorDetails

public static final void TwoRNA_SetErrorDetails(long jarg1,
                                                TwoRNA jarg1_,
                                                java.lang.String jarg2)

TwoRNA_SetTemperature

public static final int TwoRNA_SetTemperature(long jarg1,
                                              TwoRNA jarg1_,
                                              double jarg2)