/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 3.0.12
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

package ur_rna.RNAstructure.backend;

public class RNABackendJNI {
  public final static native long new_CIntVector__SWIG_0();
  public final static native long new_CIntVector__SWIG_1(long jarg1);
  public final static native long CIntVector_size(long jarg1, CIntVector jarg1_);
  public final static native long CIntVector_capacity(long jarg1, CIntVector jarg1_);
  public final static native void CIntVector_reserve(long jarg1, CIntVector jarg1_, long jarg2);
  public final static native boolean CIntVector_isEmpty(long jarg1, CIntVector jarg1_);
  public final static native void CIntVector_clear(long jarg1, CIntVector jarg1_);
  public final static native void CIntVector_add(long jarg1, CIntVector jarg1_, int jarg2);
  public final static native int CIntVector_get(long jarg1, CIntVector jarg1_, int jarg2);
  public final static native void CIntVector_set(long jarg1, CIntVector jarg1_, int jarg2, int jarg3);
  public final static native void delete_CIntVector(long jarg1);
  public final static native long new_CDblVector__SWIG_0();
  public final static native long new_CDblVector__SWIG_1(long jarg1);
  public final static native long CDblVector_size(long jarg1, CDblVector jarg1_);
  public final static native long CDblVector_capacity(long jarg1, CDblVector jarg1_);
  public final static native void CDblVector_reserve(long jarg1, CDblVector jarg1_, long jarg2);
  public final static native boolean CDblVector_isEmpty(long jarg1, CDblVector jarg1_);
  public final static native void CDblVector_clear(long jarg1, CDblVector jarg1_);
  public final static native void CDblVector_add(long jarg1, CDblVector jarg1_, double jarg2);
  public final static native double CDblVector_get(long jarg1, CDblVector jarg1_, int jarg2);
  public final static native void CDblVector_set(long jarg1, CDblVector jarg1_, int jarg2, double jarg3);
  public final static native void delete_CDblVector(long jarg1);
  public final static native long new_datatable();
  public final static native void delete_datatable(long jarg1);
  public final static native int DBN_BIT_SEQ_LABEL_get();
  public final static native int DBN_BIT_SIDE_TITLES_get();
  public final static native int DBN_BIT_MULTI_TITLE_get();
  public final static native int DBN_BIT_MULTI_SEQ_get();
  public final static native int DBN_FMT_SINGLE_TITLE_get();
  public final static native int DBN_FMT_SIDE_TITLES_get();
  public final static native int DBN_FMT_MULTI_TITLE_get();
  public final static native int DBN_FMT_MULTI_TITLE_AND_SEQ_get();
  public final static native int parseDotBracketFormat(String jarg1);
  public final static native void delete_ProgressHandler(long jarg1);
  public final static native void ProgressHandler_update__SWIG_0(long jarg1, ProgressHandler jarg1_, int jarg2);
  public final static native void ProgressHandler_update__SWIG_1(long jarg1, ProgressHandler jarg1_, double jarg2, double jarg3);
  public final static native void ProgressHandler_updateFraction(long jarg1, ProgressHandler jarg1_, double jarg2);
  public final static native boolean ProgressHandler_canceled(long jarg1, ProgressHandler jarg1_);
  public final static native void ProgressHandler_cancel(long jarg1, ProgressHandler jarg1_);
  public final static native int ProgressHandler_progress(long jarg1, ProgressHandler jarg1_);
  public final static native void ProgressHandler_reset(long jarg1, ProgressHandler jarg1_);
  public final static native long new_SimpleProgressHandler();
  public final static native void delete_SimpleProgressHandler(long jarg1);
  public final static native long new_TProgressDialog();
  public final static native void TProgressDialog_update(long jarg1, TProgressDialog jarg1_, int jarg2);
  public final static native void delete_TProgressDialog(long jarg1);
  public final static native long new_PartialProgress(long jarg1, ProgressHandler jarg1_);
  public final static native void PartialProgress_workInNextStep_set(long jarg1, PartialProgress jarg1_, int jarg2);
  public final static native int PartialProgress_workInNextStep_get(long jarg1, PartialProgress jarg1_);
  public final static native void PartialProgress_update(long jarg1, PartialProgress jarg1_, int jarg2);
  public final static native boolean PartialProgress_canceled(long jarg1, PartialProgress jarg1_);
  public final static native void PartialProgress_cancel(long jarg1, PartialProgress jarg1_);
  public final static native void PartialProgress_setNextStep(long jarg1, PartialProgress jarg1_, int jarg2);
  public final static native void PartialProgress_setWorkComplete(long jarg1, PartialProgress jarg1_, int jarg2);
  public final static native void PartialProgress_stepComplete(long jarg1, PartialProgress jarg1_);
  public final static native void PartialProgress_advanceToNextStep(long jarg1, PartialProgress jarg1_, int jarg2);
  public final static native void PartialProgress_setClient(long jarg1, PartialProgress jarg1_, long jarg2, ProgressHandler jarg2_);
  public final static native void delete_PartialProgress(long jarg1);
  public final static native double DEFAULT_SHAPE_INTERCEPT_get();
  public final static native double DEFAULT_SHAPE_SLOPE_get();
  public final static native long new_singlestructure(int jarg1);
  public final static native void singlestructure_energy_set(long jarg1, singlestructure jarg1_, int jarg2);
  public final static native int singlestructure_energy_get(long jarg1, singlestructure jarg1_);
  public final static native void singlestructure_ctlabel_set(long jarg1, singlestructure jarg1_, String jarg2);
  public final static native String singlestructure_ctlabel_get(long jarg1, singlestructure jarg1_);
  public final static native int singlestructure_getSequenceLength(long jarg1, singlestructure jarg1_);
  public final static native void singlestructure_setSequenceLength(long jarg1, singlestructure jarg1_, int jarg2);
  public final static native int singlestructure_getBasePair(long jarg1, singlestructure jarg1_, int jarg2);
  public final static native void singlestructure_setBasePair(long jarg1, singlestructure jarg1_, int jarg2, int jarg3);
  public final static native void delete_singlestructure(long jarg1);
  public final static native long new_structure__SWIG_0(int jarg1);
  public final static native long new_structure__SWIG_1();
  public final static native void delete_structure(long jarg1);
  public final static native String structure_GetCtLabel(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetEnergy(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetNumberofStructures(long jarg1, structure jarg1_);
  public final static native int structure_GetPair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native int structure_GetPair__SWIG_1(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetBase(long jarg1, structure jarg1_, int jarg2);
  public final static native String structure_GetSequenceLabel(long jarg1, structure jarg1_);
  public final static native int structure_GetSequenceLength(long jarg1, structure jarg1_);
  public final static native String structure_GetSequence(long jarg1, structure jarg1_);
  public final static native void structure_RemovePair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native void structure_RemovePair__SWIG_1(long jarg1, structure jarg1_, int jarg2);
  public final static native boolean structure_HasPseudoknots__SWIG_0(long jarg1, structure jarg1_, int jarg2);
  public final static native boolean structure_HasPseudoknots__SWIG_1(long jarg1, structure jarg1_);
  public final static native void structure_FindPseudoknots__SWIG_0(long jarg1, structure jarg1_, int jarg2, long jarg3, CIntVector jarg3_, long jarg4, CIntVector jarg4_);
  public final static native void structure_FindPseudoknots__SWIG_1(long jarg1, structure jarg1_, int jarg2, long jarg3, CIntVector jarg3_);
  public final static native void structure_FindPseudoknots__SWIG_2(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_GetPseudoknotRanks__SWIG_0(long jarg1, structure jarg1_, long jarg2, CIntVector jarg2_, int jarg3);
  public final static native void structure_GetPseudoknotRanks__SWIG_1(long jarg1, structure jarg1_, long jarg2, CIntVector jarg2_);
  public final static native void structure_BreakPseudoknots(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_SetCtLabel(long jarg1, structure jarg1_, String jarg2, int jarg3);
  public final static native void structure_SetEnergy(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native void structure_SetPair__SWIG_0(long jarg1, structure jarg1_, int jarg2, int jarg3, int jarg4);
  public final static native void structure_SetPair__SWIG_1(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native void structure_SetSequenceLabel(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_SetSequence(long jarg1, structure jarg1_, String jarg2);
  public final static native void structure_allocatetem(long jarg1, structure jarg1_);
  public final static native void structure_AddDouble(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_AddForbiddenPair(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native void structure_AddGUPair(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_AddModified(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_AddPair(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native void structure_AddSingle(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_AddDomain(long jarg1, structure jarg1_, int jarg2, int jarg3);
  public final static native boolean structure_DistanceLimited(long jarg1, structure jarg1_);
  public final static native int structure_GetDouble(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetForbiddenPair5(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetForbiddenPair3(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetGUpair(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetModified(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetNumberofDoubles(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofForbiddenPairs(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofGU(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofModified(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofSingles(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofPairs(long jarg1, structure jarg1_);
  public final static native int structure_GetNumberofDomains(long jarg1, structure jarg1_);
  public final static native int structure_GetPair5(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetPair3(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetPairingDistanceLimit(long jarg1, structure jarg1_);
  public final static native int structure_GetSingle(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_RemoveSingleStrandConstraints(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetDomain5(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_GetDomain3(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_RemoveConstraints(long jarg1, structure jarg1_);
  public final static native void structure_SetPairingDistance(long jarg1, structure jarg1_, int jarg2);
  public final static native int structure_ctout(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_writedotbracket__SWIG_0(long jarg1, structure jarg1_, String jarg2, int jarg3, int jarg4);
  public final static native int structure_writedotbracket__SWIG_1(long jarg1, structure jarg1_, String jarg2, int jarg3);
  public final static native int structure_writedotbracket__SWIG_2(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_openct(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_opendbn(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_writeseq__SWIG_0(long jarg1, structure jarg1_, String jarg2, int jarg3, boolean jarg4);
  public final static native int structure_writeseq__SWIG_1(long jarg1, structure jarg1_, String jarg2, int jarg3);
  public final static native int structure_writeseq__SWIG_2(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_openseq(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_openseqx(long jarg1, structure jarg1_, String jarg2);
  public final static native void structure_AddStructure(long jarg1, structure jarg1_);
  public final static native void structure_CleanStructure(long jarg1, structure jarg1_, int jarg2);
  public final static native void structure_RemoveLastStructure(long jarg1, structure jarg1_);
  public final static native void structure_RemoveAllStructures(long jarg1, structure jarg1_);
  public final static native void structure_RemoveStructure(long jarg1, structure jarg1_, int jarg2);
  public final static native long structure_GetThermodynamicDataTable(long jarg1, structure jarg1_);
  public final static native void structure_SetThermodynamicDataTable(long jarg1, structure jarg1_, long jarg2, datatable jarg2_);
  public final static native boolean structure_IsAlphabetLoaded(long jarg1, structure jarg1_);
  public final static native boolean structure_IsThermoDataLoaded(long jarg1, structure jarg1_);
  public final static native void structure_sort(long jarg1, structure jarg1_);
  public final static native boolean structure_ProblemwithStructures(long jarg1, structure jarg1_);
  public final static native int structure_ReadSHAPE__SWIG_0(long jarg1, structure jarg1_, String jarg2, float jarg3, float jarg4);
  public final static native int structure_ReadSHAPE__SWIG_1(long jarg1, structure jarg1_, String jarg2, int jarg3, boolean jarg4);
  public final static native int structure_ReadSHAPE__SWIG_2(long jarg1, structure jarg1_, String jarg2, int jarg3);
  public final static native int structure_ReadSHAPE__SWIG_3(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_ReadOffset(long jarg1, structure jarg1_, String jarg2, String jarg3);
  public final static native int structure_ReadExperimentalPairBonus__SWIG_0(long jarg1, structure jarg1_, String jarg2, double jarg3, double jarg4);
  public final static native int structure_ReadExperimentalPairBonus__SWIG_1(long jarg1, structure jarg1_, String jarg2, double jarg3);
  public final static native int structure_ReadExperimentalPairBonus__SWIG_2(long jarg1, structure jarg1_, String jarg2);
  public final static native int structure_WriteSHAPE__SWIG_0(long jarg1, structure jarg1_, String jarg2, boolean jarg3);
  public final static native int structure_WriteSHAPE__SWIG_1(long jarg1, structure jarg1_, String jarg2);
  public final static native void structure_DeleteSHAPE(long jarg1, structure jarg1_);
  public final static native void structure_AllocateSHAPE(long jarg1, structure jarg1_);
  public final static native void structure_allocateconstant(long jarg1, structure jarg1_);
  public final static native void structure_SHAPEFileRead_set(long jarg1, structure jarg1_, boolean jarg2);
  public final static native boolean structure_SHAPEFileRead_get(long jarg1, structure jarg1_);
  public final static native String structure_GetErrorDetails(long jarg1, structure jarg1_);
  public final static native boolean structure_IsNuc__SWIG_0(long jarg1, structure jarg1_, int jarg2, char jarg3);
  public final static native boolean structure_IsNuc__SWIG_1(long jarg1, structure jarg1_, int jarg2, char jarg3, long jarg4, datatable jarg4_);
  public final static native void structure_RemoveEnergyLabels__SWIG_0(long jarg1, structure jarg1_, String jarg2);
  public final static native void structure_RemoveEnergyLabels__SWIG_1(long jarg1, structure jarg1_);
  public final static native long structure_generate_constraint_matrix(long jarg1, structure jarg1_);
  public final static native void structure_ShowWarnings_set(int jarg1);
  public final static native int structure_ShowWarnings_get();
  public final static native void structure_SumShapeRepeats_set(boolean jarg1);
  public final static native boolean structure_SumShapeRepeats_get();
  public final static native boolean hasPseudoknots(long jarg1, CIntVector jarg1_);
  public final static native void findPseudoknots__SWIG_0(long jarg1, CIntVector jarg1_, long jarg2, CIntVector jarg2_, long jarg3, CIntVector jarg3_);
  public final static native void findPseudoknots__SWIG_1(long jarg1, CIntVector jarg1_, long jarg2, CIntVector jarg2_);
  public final static native void findPseudoknots__SWIG_2(long jarg1, CIntVector jarg1_);
  public final static native long new_Thermodynamics__SWIG_0(boolean jarg1, String jarg2, double jarg3);
  public final static native long new_Thermodynamics__SWIG_1(boolean jarg1, String jarg2);
  public final static native long new_Thermodynamics__SWIG_2(boolean jarg1);
  public final static native long new_Thermodynamics__SWIG_3();
  public final static native long new_Thermodynamics__SWIG_4(long jarg1, Thermodynamics jarg1_);
  public final static native int Thermodynamics_SetTemperature(long jarg1, Thermodynamics jarg1_, double jarg2);
  public final static native double Thermodynamics_GetTemperature(long jarg1, Thermodynamics jarg1_);
  public final static native String Thermodynamics_GetAlphabetName(long jarg1, Thermodynamics jarg1_);
  public final static native int Thermodynamics_ReadThermodynamic__SWIG_0(long jarg1, Thermodynamics jarg1_, String jarg2, String jarg3, double jarg4);
  public final static native int Thermodynamics_ReadThermodynamic__SWIG_1(long jarg1, Thermodynamics jarg1_, String jarg2, String jarg3);
  public final static native int Thermodynamics_ReadThermodynamic__SWIG_2(long jarg1, Thermodynamics jarg1_, String jarg2);
  public final static native int Thermodynamics_ReadThermodynamic__SWIG_3(long jarg1, Thermodynamics jarg1_);
  public final static native int Thermodynamics_ReloadDataTables__SWIG_0(long jarg1, Thermodynamics jarg1_, double jarg2);
  public final static native int Thermodynamics_ReloadDataTables__SWIG_1(long jarg1, Thermodynamics jarg1_);
  public final static native boolean Thermodynamics_VerifyThermodynamic(long jarg1, Thermodynamics jarg1_);
  public final static native long Thermodynamics_GetDatatable(long jarg1, Thermodynamics jarg1_);
  public final static native long Thermodynamics_GetEnthalpyTable__SWIG_0(long jarg1, Thermodynamics jarg1_, String jarg2);
  public final static native long Thermodynamics_GetEnthalpyTable__SWIG_1(long jarg1, Thermodynamics jarg1_);
  public final static native void Thermodynamics_ClearEnergies(long jarg1, Thermodynamics jarg1_);
  public final static native void Thermodynamics_ClearEnthalpies(long jarg1, Thermodynamics jarg1_);
  public final static native boolean Thermodynamics_GetEnergyRead(long jarg1, Thermodynamics jarg1_);
  public final static native boolean Thermodynamics_IsAlphabetRead(long jarg1, Thermodynamics jarg1_);
  public final static native void delete_Thermodynamics(long jarg1);
  public final static native void Thermodynamics_isrna_set(long jarg1, Thermodynamics jarg1_, boolean jarg2);
  public final static native boolean Thermodynamics_isrna_get(long jarg1, Thermodynamics jarg1_);
  public final static native int SEQUENCE_STRING_get();
  public final static native int FILE_CT_get();
  public final static native int FILE_SEQ_get();
  public final static native int FILE_PFS_get();
  public final static native int FILE_SAV_get();
  public final static native int FILE_DBN_get();
  public final static native long new_RNA__SWIG_0(String jarg1, boolean jarg2);
  public final static native long new_RNA__SWIG_1(String jarg1);
  public final static native long new_RNA__SWIG_2(String jarg1, int jarg2, String jarg3, boolean jarg4, boolean jarg5);
  public final static native long new_RNA__SWIG_3(String jarg1, int jarg2, String jarg3, boolean jarg4);
  public final static native long new_RNA__SWIG_4(String jarg1, int jarg2, String jarg3);
  public final static native long new_RNA__SWIG_5(String jarg1, int jarg2, long jarg3, Thermodynamics jarg3_);
  public final static native long new_RNA__SWIG_6(String jarg1, int jarg2, boolean jarg3);
  public final static native long new_RNA__SWIG_7(String jarg1, int jarg2);
  public final static native long new_RNA__SWIG_8(boolean jarg1);
  public final static native long new_RNA__SWIG_9();
  public final static native int RNA_GetErrorCode(long jarg1, RNA jarg1_);
  public final static native String RNA_GetErrorMessage(int jarg1);
  public final static native String RNA_GetFullErrorMessage(long jarg1, RNA jarg1_);
  public final static native String RNA_GetErrorDetails(long jarg1, RNA jarg1_);
  public final static native void RNA_SetErrorDetails(long jarg1, RNA jarg1_, String jarg2);
  public final static native void RNA_SetSequenceLabel(long jarg1, RNA jarg1_, String jarg2);
  public final static native void RNA_ResetError(long jarg1, RNA jarg1_);
  public final static native void RNA_EnsureStructureCapcacity(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_SpecifyPair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, int jarg4);
  public final static native int RNA_SpecifyPair__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_RemovePairs__SWIG_0(long jarg1, RNA jarg1_, int jarg2, boolean jarg3);
  public final static native int RNA_RemovePairs__SWIG_1(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_RemovePairs__SWIG_2(long jarg1, RNA jarg1_);
  public final static native int RNA_RemoveBasePair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_RemoveBasePair__SWIG_1(long jarg1, RNA jarg1_, int jarg2);
  public final static native double RNA_CalculateFreeEnergy__SWIG_0(long jarg1, RNA jarg1_, int jarg2, boolean jarg3);
  public final static native double RNA_CalculateFreeEnergy__SWIG_1(long jarg1, RNA jarg1_, int jarg2);
  public final static native double RNA_CalculateFreeEnergy__SWIG_2(long jarg1, RNA jarg1_);
  public final static native double RNA_ExteriorLoopCorrection(long jarg1, RNA jarg1_, int jarg2, boolean jarg3, int jarg4, int jarg5);
  public final static native int RNA_WriteThermodynamicDetails__SWIG_0(long jarg1, RNA jarg1_, String jarg2, boolean jarg3);
  public final static native int RNA_WriteThermodynamicDetails__SWIG_1(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_FoldSingleStrand__SWIG_0(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5, int jarg6, boolean jarg7, boolean jarg8, boolean jarg9);
  public final static native int RNA_FoldSingleStrand__SWIG_1(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5, int jarg6, boolean jarg7, boolean jarg8);
  public final static native int RNA_FoldSingleStrand__SWIG_2(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5, int jarg6, boolean jarg7);
  public final static native int RNA_FoldSingleStrand__SWIG_3(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5, int jarg6);
  public final static native int RNA_FoldSingleStrand__SWIG_4(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5);
  public final static native int RNA_FoldSingleStrand__SWIG_5(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4);
  public final static native int RNA_FoldSingleStrand__SWIG_6(long jarg1, RNA jarg1_, float jarg2, int jarg3);
  public final static native int RNA_FoldSingleStrand__SWIG_7(long jarg1, RNA jarg1_, float jarg2);
  public final static native int RNA_FoldSingleStrand__SWIG_8(long jarg1, RNA jarg1_);
  public final static native int RNA_GenerateAllSuboptimalStructures__SWIG_0(long jarg1, RNA jarg1_, float jarg2, double jarg3);
  public final static native int RNA_GenerateAllSuboptimalStructures__SWIG_1(long jarg1, RNA jarg1_, float jarg2);
  public final static native int RNA_GenerateAllSuboptimalStructures__SWIG_2(long jarg1, RNA jarg1_);
  public final static native int RNA_MaximizeExpectedAccuracy__SWIG_0(long jarg1, RNA jarg1_, double jarg2, int jarg3, int jarg4, double jarg5);
  public final static native int RNA_MaximizeExpectedAccuracy__SWIG_1(long jarg1, RNA jarg1_, double jarg2, int jarg3, int jarg4);
  public final static native int RNA_MaximizeExpectedAccuracy__SWIG_2(long jarg1, RNA jarg1_, double jarg2, int jarg3);
  public final static native int RNA_MaximizeExpectedAccuracy__SWIG_3(long jarg1, RNA jarg1_, double jarg2);
  public final static native int RNA_MaximizeExpectedAccuracy__SWIG_4(long jarg1, RNA jarg1_);
  public final static native int RNA_PartitionFunction__SWIG_0(long jarg1, RNA jarg1_, String jarg2, double jarg3, boolean jarg4, boolean jarg5);
  public final static native int RNA_PartitionFunction__SWIG_1(long jarg1, RNA jarg1_, String jarg2, double jarg3, boolean jarg4);
  public final static native int RNA_PartitionFunction__SWIG_2(long jarg1, RNA jarg1_, String jarg2, double jarg3);
  public final static native int RNA_PartitionFunction__SWIG_3(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_PartitionFunction__SWIG_4(long jarg1, RNA jarg1_);
  public final static native int RNA_PredictProbablePairs__SWIG_0(long jarg1, RNA jarg1_, float jarg2);
  public final static native int RNA_PredictProbablePairs__SWIG_1(long jarg1, RNA jarg1_);
  public final static native int RNA_ProbKnot__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, double jarg4);
  public final static native int RNA_ProbKnot__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_ProbKnot__SWIG_2(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ProbKnot__SWIG_3(long jarg1, RNA jarg1_);
  public final static native int RNA_ProbKnotFromSample__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, double jarg4);
  public final static native int RNA_ProbKnotFromSample__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_ProbKnotFromSample__SWIG_2(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ProbKnotFromSample__SWIG_3(long jarg1, RNA jarg1_);
  public final static native int RNA_ReFoldSingleStrand__SWIG_0(long jarg1, RNA jarg1_, float jarg2, int jarg3, int jarg4);
  public final static native int RNA_ReFoldSingleStrand__SWIG_1(long jarg1, RNA jarg1_, float jarg2, int jarg3);
  public final static native int RNA_ReFoldSingleStrand__SWIG_2(long jarg1, RNA jarg1_, float jarg2);
  public final static native int RNA_ReFoldSingleStrand__SWIG_3(long jarg1, RNA jarg1_);
  public final static native int RNA_Stochastic__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_Stochastic__SWIG_1(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_Stochastic__SWIG_2(long jarg1, RNA jarg1_);
  public final static native int RNA_ForceDoubleStranded(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ForceFMNCleavage(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ForceMaximumPairingDistance(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ForceModification(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_ForcePair(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_ForceProhibitPair(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_ForceSingleStranded(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetForcedDoubleStranded(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetForcedFMNCleavage(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetForcedModification(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetForcedPair(long jarg1, RNA jarg1_, int jarg2, boolean jarg3);
  public final static native int RNA_GetForcedProhibitedPair(long jarg1, RNA jarg1_, int jarg2, boolean jarg3);
  public final static native int RNA_GetForcedSingleStranded(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetMaximumPairingDistance(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedDoubleStranded(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedFMNCleavages(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedModifications(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedPairs(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedProhibitedPairs(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNumberOfForcedSingleStranded(long jarg1, RNA jarg1_);
  public final static native int RNA_ReadConstraints(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_ReadSHAPE__SWIG_0(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4, int jarg5, boolean jarg6);
  public final static native int RNA_ReadSHAPE__SWIG_1(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4, int jarg5);
  public final static native int RNA_ReadSHAPE__SWIG_2(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4);
  public final static native int RNA_ReadSHAPE__SWIG_3(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4, double jarg5, double jarg6, int jarg7);
  public final static native int RNA_ReadSHAPE__SWIG_4(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4, double jarg5, double jarg6);
  public final static native int RNA_ReadDMS__SWIG_0(long jarg1, RNA jarg1_, String jarg2, boolean jarg3);
  public final static native int RNA_ReadDMS__SWIG_1(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_ReadDSO(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_ReadSSO(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_ReadExperimentalPairBonus(long jarg1, RNA jarg1_, String jarg2, double jarg3, double jarg4);
  public final static native void RNA_RemoveConstraints(long jarg1, RNA jarg1_);
  public final static native void RNA_SetConstraints(long jarg1, RNA jarg1_, long jarg2, CIntVector jarg2_);
  public final static native int RNA_SetExtrinsic(long jarg1, RNA jarg1_, int jarg2, int jarg3, double jarg4);
  public final static native int RNA_WriteConstraints(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_AddComment__SWIG_0(long jarg1, RNA jarg1_, String jarg2, int jarg3);
  public final static native int RNA_AddComment__SWIG_1(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_WriteCt(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_WriteDotBracket__SWIG_0(long jarg1, RNA jarg1_, String jarg2, int jarg3, int jarg4);
  public final static native int RNA_WriteDotBracket__SWIG_1(long jarg1, RNA jarg1_, String jarg2, int jarg3);
  public final static native int RNA_WriteDotBracket__SWIG_2(long jarg1, RNA jarg1_, String jarg2);
  public final static native int RNA_BreakPseudoknot__SWIG_0(long jarg1, RNA jarg1_, boolean jarg2, int jarg3, boolean jarg4);
  public final static native int RNA_BreakPseudoknot__SWIG_1(long jarg1, RNA jarg1_, boolean jarg2, int jarg3);
  public final static native int RNA_BreakPseudoknot__SWIG_2(long jarg1, RNA jarg1_, boolean jarg2);
  public final static native int RNA_BreakPseudoknot__SWIG_3(long jarg1, RNA jarg1_);
  public final static native boolean RNA_ContainsPseudoknot(long jarg1, RNA jarg1_, int jarg2);
  public final static native double RNA_GetEnsembleEnergy(long jarg1, RNA jarg1_);
  public final static native double RNA_GetEnsembleDefect__SWIG_0(long jarg1, RNA jarg1_, int jarg2);
  public final static native double RNA_GetEnsembleDefect__SWIG_1(long jarg1, RNA jarg1_);
  public final static native double RNA_GetFreeEnergy(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetPair__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_GetPair__SWIG_1(long jarg1, RNA jarg1_, int jarg2);
  public final static native double RNA_GetPairEnergy(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native double RNA_GetPairProbability(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native int RNA_GetPairProbabilities(long jarg1, RNA jarg1_, double[] jarg2, int jarg3);
  public final static native int RNA_GetStructureNumber(long jarg1, RNA jarg1_);
  public final static native int RNA_DetermineDrawingCoordinates__SWIG_0(long jarg1, RNA jarg1_, int jarg2, int jarg3, int jarg4);
  public final static native int RNA_DetermineDrawingCoordinates__SWIG_1(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native String RNA_GetCommentString__SWIG_0(long jarg1, RNA jarg1_, int jarg2);
  public final static native String RNA_GetCommentString__SWIG_1(long jarg1, RNA jarg1_);
  public final static native int RNA_GetNucleotideXCoordinate(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetNucleotideYCoordinate(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetLabelXCoordinate(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetLabelYCoordinate(long jarg1, RNA jarg1_, int jarg2);
  public final static native char RNA_GetNucleotide(long jarg1, RNA jarg1_, int jarg2);
  public final static native int RNA_GetSequenceLength(long jarg1, RNA jarg1_);
  public final static native String RNA_GetSequence__SWIG_0(long jarg1, RNA jarg1_);
  public final static native String RNA_GetSequence__SWIG_1(long jarg1, RNA jarg1_, long jarg2, long jarg3);
  public final static native String RNA_GetSequence__SWIG_2(long jarg1, RNA jarg1_, long jarg2);
  public final static native boolean RNA_GetBackboneType(long jarg1, RNA jarg1_);
  public final static native double RNA_GetVprimeQ(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native double RNA_GetW(long jarg1, RNA jarg1_, int jarg2, int jarg3);
  public final static native long RNA_GetStructure(long jarg1, RNA jarg1_);
  public final static native void RNA_SetProgress(long jarg1, RNA jarg1_, long jarg2, ProgressHandler jarg2_);
  public final static native void RNA_StopProgress(long jarg1, RNA jarg1_);
  public final static native long RNA_GetProgress(long jarg1, RNA jarg1_);
  public final static native void delete_RNA(long jarg1);
  public final static native void RNA_CopyThermo(long jarg1, RNA jarg1_, long jarg2, Thermodynamics jarg2_);
  public final static native int RNA_getInts(long jarg1, RNA jarg1_, int[] jarg2, int jarg3);
  public final static native void RNA_initInts(long jarg1, RNA jarg1_);
  public final static native int RNA_getIntAt(long jarg1, RNA jarg1_, int jarg2);
  public final static native int COMPOUNDMESSAGELENGTH_get();
  public final static native long new_TwoRNA__SWIG_0(String jarg1, String jarg2, boolean jarg3);
  public final static native long new_TwoRNA__SWIG_1(String jarg1, String jarg2);
  public final static native long new_TwoRNA__SWIG_2(String jarg1, int jarg2, String jarg3, int jarg4, boolean jarg5);
  public final static native long new_TwoRNA__SWIG_3(String jarg1, int jarg2, String jarg3, int jarg4);
  public final static native long new_TwoRNA__SWIG_4(String jarg1, int jarg2, String jarg3, int jarg4, long jarg5, Thermodynamics jarg5_);
  public final static native long new_TwoRNA__SWIG_5();
  public final static native int TwoRNA_SetTemperature(long jarg1, TwoRNA jarg1_, double jarg2);
  public final static native double TwoRNA_GetTemperature(long jarg1, TwoRNA jarg1_);
  public final static native int TwoRNA_GetErrorCode(long jarg1, TwoRNA jarg1_);
  public final static native String TwoRNA_GetErrorMessage(long jarg1, TwoRNA jarg1_, int jarg2);
  public final static native String TwoRNA_GetErrorDetails(long jarg1, TwoRNA jarg1_);
  public final static native void TwoRNA_SetErrorDetails(long jarg1, TwoRNA jarg1_, String jarg2);
  public final static native String TwoRNA_GetErrorMessageString(long jarg1, TwoRNA jarg1_, int jarg2);
  public final static native void TwoRNA_ResetError(long jarg1, TwoRNA jarg1_);
  public final static native long TwoRNA_GetRNA1(long jarg1, TwoRNA jarg1_);
  public final static native long TwoRNA_GetRNA2(long jarg1, TwoRNA jarg1_);
  public final static native void delete_TwoRNA(long jarg1);
  public final static native void TwoRNA_compoundmessage_set(long jarg1, TwoRNA jarg1_, String jarg2);
  public final static native String TwoRNA_compoundmessage_get(long jarg1, TwoRNA jarg1_);
  public final static native long new_HybridRNA__SWIG_0(String jarg1, String jarg2, boolean jarg3);
  public final static native long new_HybridRNA__SWIG_1(String jarg1, String jarg2);
  public final static native long new_HybridRNA__SWIG_2(String jarg1, int jarg2, String jarg3, int jarg4, boolean jarg5);
  public final static native long new_HybridRNA__SWIG_3(String jarg1, int jarg2, String jarg3, int jarg4);
  public final static native long new_HybridRNA__SWIG_4(String jarg1, int jarg2, String jarg3, int jarg4, String jarg5);
  public final static native int HybridRNA_AccessFold__SWIG_0(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4, int jarg5, int jarg6);
  public final static native int HybridRNA_AccessFold__SWIG_1(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4, int jarg5);
  public final static native int HybridRNA_AccessFold__SWIG_2(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3, int jarg4);
  public final static native int HybridRNA_AccessFold__SWIG_3(long jarg1, HybridRNA jarg1_, double jarg2, float jarg3);
  public final static native int HybridRNA_AccessFold__SWIG_4(long jarg1, HybridRNA jarg1_, double jarg2);
  public final static native int HybridRNA_AccessFold__SWIG_5(long jarg1, HybridRNA jarg1_);
  public final static native int HybridRNA_FoldBimolecular__SWIG_0(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5, int jarg6);
  public final static native int HybridRNA_FoldBimolecular__SWIG_1(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, String jarg5);
  public final static native int HybridRNA_FoldBimolecular__SWIG_2(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4);
  public final static native int HybridRNA_FoldBimolecular__SWIG_3(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3);
  public final static native int HybridRNA_FoldBimolecular__SWIG_4(long jarg1, HybridRNA jarg1_, float jarg2);
  public final static native int HybridRNA_FoldBimolecular__SWIG_5(long jarg1, HybridRNA jarg1_);
  public final static native int HybridRNA_FoldDuplex__SWIG_0(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4, int jarg5);
  public final static native int HybridRNA_FoldDuplex__SWIG_1(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3, int jarg4);
  public final static native int HybridRNA_FoldDuplex__SWIG_2(long jarg1, HybridRNA jarg1_, float jarg2, int jarg3);
  public final static native int HybridRNA_FoldDuplex__SWIG_3(long jarg1, HybridRNA jarg1_, float jarg2);
  public final static native int HybridRNA_FoldDuplex__SWIG_4(long jarg1, HybridRNA jarg1_);
  public final static native int HybridRNA_PartitionFunctionBimolecular__SWIG_0(long jarg1, HybridRNA jarg1_, String jarg2);
  public final static native int HybridRNA_PartitionFunctionBimolecular__SWIG_1(long jarg1, HybridRNA jarg1_);
  public final static native long HybridRNA_GetRNA1(long jarg1, HybridRNA jarg1_);
  public final static native long HybridRNA_GetRNA2(long jarg1, HybridRNA jarg1_);
  public final static native int HybridRNA_GetErrorCode(long jarg1, HybridRNA jarg1_);
  public final static native String HybridRNA_GetMyErrorMessage(long jarg1, HybridRNA jarg1_, int jarg2);
  public final static native boolean HybridRNA_GetForbidIntramolecular(long jarg1, HybridRNA jarg1_);
  public final static native void HybridRNA_SetForbidIntramolecular(long jarg1, HybridRNA jarg1_, boolean jarg2);
  public final static native void HybridRNA_SetProgress(long jarg1, HybridRNA jarg1_, long jarg2, ProgressHandler jarg2_);
  public final static native void HybridRNA_StopProgress(long jarg1, HybridRNA jarg1_);
  public final static native void delete_HybridRNA(long jarg1);
  public final static native long new_Dynalign_object__SWIG_0();
  public final static native long new_Dynalign_object__SWIG_1(String jarg1, String jarg2, boolean jarg3);
  public final static native long new_Dynalign_object__SWIG_2(String jarg1, String jarg2);
  public final static native long new_Dynalign_object__SWIG_3(String jarg1, int jarg2, String jarg3, int jarg4, boolean jarg5);
  public final static native long new_Dynalign_object__SWIG_4(String jarg1, int jarg2, String jarg3, int jarg4);
  public final static native long new_Dynalign_object__SWIG_5(String jarg1, int jarg2, String jarg3, int jarg4, long jarg5, Thermodynamics jarg5_);
  public final static native long new_Dynalign_object__SWIG_6(String jarg1);
  public final static native long new_Dynalign_object__SWIG_7(String jarg1, short jarg2, short jarg3, short jarg4, short jarg5);
  public final static native 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, String jarg9, boolean jarg10, short jarg11, boolean jarg12, short jarg13, int jarg14);
  public final static native 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, String jarg9, boolean jarg10, short jarg11, boolean jarg12, short jarg13);
  public final static native 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, String jarg9, boolean jarg10, short jarg11, boolean jarg12);
  public final static native 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, String jarg9, boolean jarg10, short jarg11);
  public final static native 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, String jarg9, boolean jarg10);
  public final static native 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, String jarg9);
  public final static native 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);
  public final static native int Dynalign_object_Dynalign__SWIG_7(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6, float jarg7);
  public final static native int Dynalign_object_Dynalign__SWIG_8(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5, short jarg6);
  public final static native int Dynalign_object_Dynalign__SWIG_9(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4, short jarg5);
  public final static native int Dynalign_object_Dynalign__SWIG_10(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3, short jarg4);
  public final static native int Dynalign_object_Dynalign__SWIG_11(long jarg1, Dynalign_object jarg1_, short jarg2, short jarg3);
  public final static native int Dynalign_object_Dynalign__SWIG_12(long jarg1, Dynalign_object jarg1_, short jarg2);
  public final static native int Dynalign_object_Dynalign__SWIG_13(long jarg1, Dynalign_object jarg1_);
  public final static native void Dynalign_object_WriteAlignment(long jarg1, Dynalign_object jarg1_, String jarg2);
  public final static native int Dynalign_object_ForceAlignment(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3);
  public final static native int Dynalign_object_GetForcedAlignment(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3);
  public final static native int Dynalign_object_ReadAlignmentConstraints(long jarg1, Dynalign_object jarg1_, String jarg2);
  public final static native int Dynalign_object_Templatefromct(long jarg1, Dynalign_object jarg1_, String jarg2);
  public final static native int Dynalign_object_Templatefromdsv(long jarg1, Dynalign_object jarg1_, String jarg2, float jarg3);
  public final static native double Dynalign_object_GetBestPairEnergy(long jarg1, Dynalign_object jarg1_, int jarg2, int jarg3, int jarg4);
  public final static native double Dynalign_object_GetLowestEnergy(long jarg1, Dynalign_object jarg1_);
  public final static native String Dynalign_object_GetErrorMessage(long jarg1, Dynalign_object jarg1_, int jarg2);
  public final static native void Dynalign_object_SetProgress(long jarg1, Dynalign_object jarg1_, long jarg2, ProgressHandler jarg2_);
  public final static native void Dynalign_object_StopProgress(long jarg1, Dynalign_object jarg1_);
  public final static native void delete_Dynalign_object(long jarg1);
  public final static native String getDataPath__SWIG_0(String jarg1);
  public final static native String getDataPath__SWIG_1();
  public final static native void setDataPath(String jarg1);
  public final static native long SimpleProgressHandler_SWIGUpcast(long jarg1);
  public final static native long TProgressDialog_SWIGUpcast(long jarg1);
  public final static native long PartialProgress_SWIGUpcast(long jarg1);
  public final static native long RNA_SWIGUpcast(long jarg1);
  public final static native long HybridRNA_SWIGUpcast(long jarg1);
  public final static native long Dynalign_object_SWIGUpcast(long jarg1);
}
