ur_rna.RNAstructureUI

Class RNAstructureBackendCalculatorProxyJNI

java.lang.Object

ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI

public class RNAstructureBackendCalculatorProxyJNI
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
RNAstructureBackendCalculatorProxyJNI()

Method Summary

Modifier and Type	Method and Description
static void	delete_RNAstructureBackendCalculator(long jarg1)
static long	new_RNAstructureBackendCalculator()
static void	RNAstructureBackendCalculator_activateMultilign(long jarg1, RNAstructureBackendCalculator jarg1_)
static void	RNAstructureBackendCalculator_activateTurboFold(long jarg1, RNAstructureBackendCalculator jarg1_)
static void	RNAstructureBackendCalculator_addMultilignTuple(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3)
static void	RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, java.lang.String jarg4)
static void	RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildAccessFoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_buildAllSubDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildBifoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_buildBipartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_buildDuplexFoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_buildDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_buildEfn2DataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildFoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildMaxExpectDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_buildOligoScreenDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_buildOligoWalkDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildPartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildProbKnotDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_buildStochasticDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_cancelOperation(long jarg1, RNAstructureBackendCalculator jarg1_)
static boolean	RNAstructureBackendCalculator_canFoldOligoOligo(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static boolean	RNAstructureBackendCalculator_canFoldOligoSelf(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static void	RNAstructureBackendCalculator_clearDynalignAlignmentConstraints(long jarg1, RNAstructureBackendCalculator jarg1_)
static void	RNAstructureBackendCalculator_clearFoldingConstraints(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static void	RNAstructureBackendCalculator_deleteMultilignTuple(long jarg1, RNAstructureBackendCalculator jarg1_, long jarg2)
static void	RNAstructureBackendCalculator_deleteTurboFoldTuple(long jarg1, RNAstructureBackendCalculator jarg1_, long jarg2)
static int	RNAstructureBackendCalculator_determineOligoMaximum(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static void	RNAstructureBackendCalculator_foldOligo(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, boolean jarg4, boolean jarg5, java.lang.String jarg6)
static java.lang.String	RNAstructureBackendCalculator_getAllOligoData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static java.lang.String	RNAstructureBackendCalculator_getDisplayedOligo(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static java.lang.String	RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getDynalignStructureWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getEnvVar(java.lang.String jarg1)
static int	RNAstructureBackendCalculator_GetErrorCode(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getFoldingConstraints(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static int	RNAstructureBackendCalculator_getFoldWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_GetFullErrorMessage(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getGraphRegionBegin(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getGraphRegionEnd(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getMaxConstraintIndex(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static int	RNAstructureBackendCalculator_getMaxLoop(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getMaxPair(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getMostStableOligo(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getMultilignCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static int	RNAstructureBackendCalculator_getMultilignMaxPairs(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getMultilignSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getNumMultilignSequences(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getNumTurboFoldSequences(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getOligoLabelData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static int	RNAstructureBackendCalculator_getOligoTargetLength(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getOligoTargetSequence(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getProgressNumber(long jarg1, RNAstructureBackendCalculator jarg1_)
static int	RNAstructureBackendCalculator_getRefoldWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getSaveFile(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getStructureType(long jarg1, RNAstructureBackendCalculator jarg1_)
static double	RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff(long jarg1, RNAstructureBackendCalculator jarg1_)
static float	RNAstructureBackendCalculator_getSuboptimalPercentDiff(long jarg1, RNAstructureBackendCalculator jarg1_)
static double	RNAstructureBackendCalculator_getTemperature(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getTurboFoldCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static java.lang.String	RNAstructureBackendCalculator_getTurboFoldSaveFile(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static java.lang.String	RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_)
static java.lang.String	RNAstructureBackendCalculator_getVersion()
static java.lang.String	RNAstructureBackendCalculator_loadDoubleRNA__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4, int jarg5)
static java.lang.String	RNAstructureBackendCalculator_loadDoubleRNA__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_loadSingleRNA__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3, int jarg4)
static java.lang.String	RNAstructureBackendCalculator_loadSingleRNA__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_readFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3)
static void	RNAstructureBackendCalculator_readSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_runAccessFold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, float jarg3, int jarg4, double jarg5, int jarg6, boolean jarg7)
static java.lang.String	RNAstructureBackendCalculator_runAllSub(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, float jarg3, double jarg4)
static java.lang.String	RNAstructureBackendCalculator_runBifold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, float jarg3, int jarg4, int jarg5, boolean jarg6, boolean jarg7)
static java.lang.String	RNAstructureBackendCalculator_runBipartition(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_runDuplexFold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, float jarg3, int jarg4, int jarg5, boolean jarg6)
static java.lang.String	RNAstructureBackendCalculator_runDynalign(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, java.lang.String jarg4, java.lang.String jarg5, double jarg6, int jarg7, int jarg8, int jarg9, float jarg10, boolean jarg11)
static java.lang.String	RNAstructureBackendCalculator_runDynalignRefold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, java.lang.String jarg4, int jarg5, int jarg6, int jarg7, int jarg8)
static java.lang.String	RNAstructureBackendCalculator_runEfn2(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_runFold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, int jarg4, int jarg5, boolean jarg6)
static java.lang.String	RNAstructureBackendCalculator_runMaxExpect(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, double jarg3, int jarg4, int jarg5, double jarg6)
static java.lang.String	RNAstructureBackendCalculator_runMultilign(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5, double jarg6, boolean jarg7, double jarg8, int jarg9, int jarg10, java.lang.String jarg11, boolean jarg12, boolean jarg13)
static java.lang.String	RNAstructureBackendCalculator_runOligoScreen(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, java.lang.String jarg3, boolean jarg4)
static java.lang.String	RNAstructureBackendCalculator_runOligoWalk(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, java.lang.String jarg4, boolean jarg5, int jarg6, int jarg7, java.lang.String jarg8, int jarg9, int jarg10)
static java.lang.String	RNAstructureBackendCalculator_runPartition(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_runPseudoknotPrediction(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, int jarg4)
static java.lang.String	RNAstructureBackendCalculator_runPseudoknotRemoval(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, boolean jarg3)
static java.lang.String	RNAstructureBackendCalculator_runRefold(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, int jarg4, int jarg5)
static java.lang.String	RNAstructureBackendCalculator_runStochastic(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3, int jarg4)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4, int jarg5, int jarg6, double jarg7, java.lang.String jarg8)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4, int jarg5, int jarg6, double jarg7)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, int jarg4, int jarg5, java.lang.String jarg6)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, int jarg4, int jarg5)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_0(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4, java.lang.String jarg5)
static java.lang.String	RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_1(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4)
static java.lang.String	RNAstructureBackendCalculator_setCleavedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)
static java.lang.String	RNAstructureBackendCalculator_setDoubleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)
static java.lang.String	RNAstructureBackendCalculator_setDynalignAlignmentConstraint(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)
static int	RNAstructureBackendCalculator_setEnvVar(java.lang.String jarg1)
static java.lang.String	RNAstructureBackendCalculator_setForcedHelix(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5)
static void	RNAstructureBackendCalculator_setMaxLoop(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static void	RNAstructureBackendCalculator_setMaxPair(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)
static java.lang.String	RNAstructureBackendCalculator_setModifiedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)
static java.lang.String	RNAstructureBackendCalculator_setProhibitedHelix(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5)
static void	RNAstructureBackendCalculator_setSaveFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_setSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_setSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_setSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_setSHAPEFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static void	RNAstructureBackendCalculator_setSHAPEParam1(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2)
static void	RNAstructureBackendCalculator_setSHAPEParam2(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2)
static void	RNAstructureBackendCalculator_setSHAPEType(long jarg1, RNAstructureBackendCalculator jarg1_, boolean jarg2)
static java.lang.String	RNAstructureBackendCalculator_setSingleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)
static void	RNAstructureBackendCalculator_setTemperature(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2)
static boolean	RNAstructureBackendCalculator_wasCanceled(long jarg1, RNAstructureBackendCalculator jarg1_)
static void	RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_writeFastaFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)
static java.lang.String	RNAstructureBackendCalculator_writeFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2, int jarg3)
static java.lang.String	RNAstructureBackendCalculator_writeSequenceFile(long jarg1, RNAstructureBackendCalculator jarg1_, java.lang.String jarg2)

Methods inherited from class java.lang.Object

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

Constructor Detail

RNAstructureBackendCalculatorProxyJNI

public RNAstructureBackendCalculatorProxyJNI()

Method Detail

delete_RNAstructureBackendCalculator

public static final void delete_RNAstructureBackendCalculator(long jarg1)

new_RNAstructureBackendCalculator

public static final long new_RNAstructureBackendCalculator()

RNAstructureBackendCalculator_activateMultilign

public static final void RNAstructureBackendCalculator_activateMultilign(long jarg1,
                                                                         RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_activateTurboFold

public static final void RNAstructureBackendCalculator_activateTurboFold(long jarg1,
                                                                         RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_addMultilignTuple

public static final void RNAstructureBackendCalculator_addMultilignTuple(long jarg1,
                                                                         RNAstructureBackendCalculator jarg1_,
                                                                         java.lang.String jarg2,
                                                                         java.lang.String jarg3)

RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_0

public static final void RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_0(long jarg1,
                                                                                 RNAstructureBackendCalculator jarg1_,
                                                                                 java.lang.String jarg2,
                                                                                 java.lang.String jarg3,
                                                                                 java.lang.String jarg4)

RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_1

public static final void RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_1(long jarg1,
                                                                                 RNAstructureBackendCalculator jarg1_,
                                                                                 java.lang.String jarg2,
                                                                                 java.lang.String jarg3)

RNAstructureBackendCalculator_buildAccessFoldDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildAccessFoldDataStructure(long jarg1,
                                                                                                RNAstructureBackendCalculator jarg1_,
                                                                                                java.lang.String jarg2,
                                                                                                java.lang.String jarg3,
                                                                                                boolean jarg4)

RNAstructureBackendCalculator_buildAllSubDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildAllSubDataStructure(long jarg1,
                                                                                            RNAstructureBackendCalculator jarg1_,
                                                                                            java.lang.String jarg2,
                                                                                            boolean jarg3)

RNAstructureBackendCalculator_buildBifoldDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildBifoldDataStructure(long jarg1,
                                                                                            RNAstructureBackendCalculator jarg1_,
                                                                                            java.lang.String jarg2,
                                                                                            java.lang.String jarg3,
                                                                                            boolean jarg4)

RNAstructureBackendCalculator_buildBipartitionDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildBipartitionDataStructure(long jarg1,
                                                                                                 RNAstructureBackendCalculator jarg1_,
                                                                                                 java.lang.String jarg2,
                                                                                                 java.lang.String jarg3,
                                                                                                 boolean jarg4)

RNAstructureBackendCalculator_buildDuplexFoldDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildDuplexFoldDataStructure(long jarg1,
                                                                                                RNAstructureBackendCalculator jarg1_,
                                                                                                java.lang.String jarg2,
                                                                                                java.lang.String jarg3,
                                                                                                boolean jarg4)

RNAstructureBackendCalculator_buildDynalignDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildDynalignDataStructure(long jarg1,
                                                                                              RNAstructureBackendCalculator jarg1_,
                                                                                              java.lang.String jarg2,
                                                                                              java.lang.String jarg3,
                                                                                              boolean jarg4)

RNAstructureBackendCalculator_buildEfn2DataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildEfn2DataStructure(long jarg1,
                                                                                          RNAstructureBackendCalculator jarg1_,
                                                                                          java.lang.String jarg2,
                                                                                          boolean jarg3)

RNAstructureBackendCalculator_buildFoldDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildFoldDataStructure(long jarg1,
                                                                                          RNAstructureBackendCalculator jarg1_,
                                                                                          java.lang.String jarg2,
                                                                                          boolean jarg3)

RNAstructureBackendCalculator_buildMaxExpectDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildMaxExpectDataStructure(long jarg1,
                                                                                               RNAstructureBackendCalculator jarg1_,
                                                                                               java.lang.String jarg2)

RNAstructureBackendCalculator_buildOligoScreenDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildOligoScreenDataStructure(long jarg1,
                                                                                                 RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_buildOligoWalkDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildOligoWalkDataStructure(long jarg1,
                                                                                               RNAstructureBackendCalculator jarg1_,
                                                                                               java.lang.String jarg2,
                                                                                               boolean jarg3)

RNAstructureBackendCalculator_buildPartitionDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildPartitionDataStructure(long jarg1,
                                                                                               RNAstructureBackendCalculator jarg1_,
                                                                                               java.lang.String jarg2,
                                                                                               boolean jarg3)

RNAstructureBackendCalculator_buildProbKnotDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildProbKnotDataStructure(long jarg1,
                                                                                              RNAstructureBackendCalculator jarg1_,
                                                                                              java.lang.String jarg2)

RNAstructureBackendCalculator_buildRefoldDynalignDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long jarg1,
                                                                                                    RNAstructureBackendCalculator jarg1_,
                                                                                                    java.lang.String jarg2)

RNAstructureBackendCalculator_buildRefoldSingleDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long jarg1,
                                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                                  java.lang.String jarg2)

RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long jarg1,
                                                                                                       RNAstructureBackendCalculator jarg1_,
                                                                                                       java.lang.String jarg2,
                                                                                                       boolean jarg3)

RNAstructureBackendCalculator_buildStochasticDataStructure

public static final java.lang.String RNAstructureBackendCalculator_buildStochasticDataStructure(long jarg1,
                                                                                                RNAstructureBackendCalculator jarg1_,
                                                                                                java.lang.String jarg2)

RNAstructureBackendCalculator_cancelOperation

public static final void RNAstructureBackendCalculator_cancelOperation(long jarg1,
                                                                       RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_canFoldOligoOligo

public static final boolean RNAstructureBackendCalculator_canFoldOligoOligo(long jarg1,
                                                                            RNAstructureBackendCalculator jarg1_,
                                                                            int jarg2)

RNAstructureBackendCalculator_canFoldOligoSelf

public static final boolean RNAstructureBackendCalculator_canFoldOligoSelf(long jarg1,
                                                                           RNAstructureBackendCalculator jarg1_,
                                                                           int jarg2)

RNAstructureBackendCalculator_clearDynalignAlignmentConstraints

public static final void RNAstructureBackendCalculator_clearDynalignAlignmentConstraints(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_clearFoldingConstraints

public static final void RNAstructureBackendCalculator_clearFoldingConstraints(long jarg1,
                                                                               RNAstructureBackendCalculator jarg1_,
                                                                               int jarg2)

RNAstructureBackendCalculator_deleteMultilignTuple

public static final void RNAstructureBackendCalculator_deleteMultilignTuple(long jarg1,
                                                                            RNAstructureBackendCalculator jarg1_,
                                                                            long jarg2)

RNAstructureBackendCalculator_deleteTurboFoldTuple

public static final void RNAstructureBackendCalculator_deleteTurboFoldTuple(long jarg1,
                                                                            RNAstructureBackendCalculator jarg1_,
                                                                            long jarg2)

RNAstructureBackendCalculator_determineOligoMaximum

public static final int RNAstructureBackendCalculator_determineOligoMaximum(long jarg1,
                                                                            RNAstructureBackendCalculator jarg1_,
                                                                            int jarg2)

RNAstructureBackendCalculator_foldOligo

public static final void RNAstructureBackendCalculator_foldOligo(long jarg1,
                                                                 RNAstructureBackendCalculator jarg1_,
                                                                 java.lang.String jarg2,
                                                                 int jarg3,
                                                                 boolean jarg4,
                                                                 boolean jarg5,
                                                                 java.lang.String jarg6)

RNAstructureBackendCalculator_getAllOligoData

public static final java.lang.String RNAstructureBackendCalculator_getAllOligoData(long jarg1,
                                                                                   RNAstructureBackendCalculator jarg1_,
                                                                                   int jarg2)

RNAstructureBackendCalculator_getDisplayedOligo

public static final java.lang.String RNAstructureBackendCalculator_getDisplayedOligo(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_,
                                                                                     int jarg2)

RNAstructureBackendCalculator_getDynalignAlignmentConstraints

public static final java.lang.String RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long jarg1,
                                                                                                   RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getDynalignAlignmentWindowSize

public static final int RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getDynalignStructureWindowSize

public static final int RNAstructureBackendCalculator_getDynalignStructureWindowSize(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getEnvVar

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

RNAstructureBackendCalculator_GetErrorCode

public static final int RNAstructureBackendCalculator_GetErrorCode(long jarg1,
                                                                   RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getFoldingConstraints

public static final java.lang.String RNAstructureBackendCalculator_getFoldingConstraints(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_,
                                                                                         int jarg2)

RNAstructureBackendCalculator_getFoldWindowSize

public static final int RNAstructureBackendCalculator_getFoldWindowSize(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_GetFullErrorMessage

public static final java.lang.String RNAstructureBackendCalculator_GetFullErrorMessage(long jarg1,
                                                                                       RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getGraphRegionBegin

public static final int RNAstructureBackendCalculator_getGraphRegionBegin(long jarg1,
                                                                          RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getGraphRegionEnd

public static final int RNAstructureBackendCalculator_getGraphRegionEnd(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getMaxConstraintIndex

public static final int RNAstructureBackendCalculator_getMaxConstraintIndex(long jarg1,
                                                                            RNAstructureBackendCalculator jarg1_,
                                                                            int jarg2)

RNAstructureBackendCalculator_getMaxLoop

public static final int RNAstructureBackendCalculator_getMaxLoop(long jarg1,
                                                                 RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getMaxPair

public static final int RNAstructureBackendCalculator_getMaxPair(long jarg1,
                                                                 RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getMostStableOligo

public static final int RNAstructureBackendCalculator_getMostStableOligo(long jarg1,
                                                                         RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getMultilignCT

public static final java.lang.String RNAstructureBackendCalculator_getMultilignCT(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  int jarg2)

RNAstructureBackendCalculator_getMultilignMaxPairs

public static final int RNAstructureBackendCalculator_getMultilignMaxPairs(long jarg1,
                                                                           RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getMultilignSequenceSetData

public static final java.lang.String RNAstructureBackendCalculator_getMultilignSequenceSetData(long jarg1,
                                                                                               RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getNumMultilignSequences

public static final int RNAstructureBackendCalculator_getNumMultilignSequences(long jarg1,
                                                                               RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getNumTurboFoldSequences

public static final int RNAstructureBackendCalculator_getNumTurboFoldSequences(long jarg1,
                                                                               RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getOligoLabelData

public static final java.lang.String RNAstructureBackendCalculator_getOligoLabelData(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_,
                                                                                     int jarg2)

RNAstructureBackendCalculator_getOligoTargetLength

public static final int RNAstructureBackendCalculator_getOligoTargetLength(long jarg1,
                                                                           RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getOligoTargetSequence

public static final java.lang.String RNAstructureBackendCalculator_getOligoTargetSequence(long jarg1,
                                                                                          RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getProgressNumber

public static final int RNAstructureBackendCalculator_getProgressNumber(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getRefoldWindowSize

public static final int RNAstructureBackendCalculator_getRefoldWindowSize(long jarg1,
                                                                          RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSaveFile

public static final java.lang.String RNAstructureBackendCalculator_getSaveFile(long jarg1,
                                                                               RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSequenceComment

public static final java.lang.String RNAstructureBackendCalculator_getSequenceComment(long jarg1,
                                                                                      RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSequenceData

public static final java.lang.String RNAstructureBackendCalculator_getSequenceData(long jarg1,
                                                                                   RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSequenceTitle

public static final java.lang.String RNAstructureBackendCalculator_getSequenceTitle(long jarg1,
                                                                                    RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getStructureType

public static final java.lang.String RNAstructureBackendCalculator_getStructureType(long jarg1,
                                                                                    RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff

public static final double RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff(long jarg1,
                                                                                   RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getSuboptimalPercentDiff

public static final float RNAstructureBackendCalculator_getSuboptimalPercentDiff(long jarg1,
                                                                                 RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getTemperature

public static final double RNAstructureBackendCalculator_getTemperature(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getTurboFoldCT

public static final java.lang.String RNAstructureBackendCalculator_getTurboFoldCT(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  int jarg2)

RNAstructureBackendCalculator_getTurboFoldSaveFile

public static final java.lang.String RNAstructureBackendCalculator_getTurboFoldSaveFile(long jarg1,
                                                                                        RNAstructureBackendCalculator jarg1_,
                                                                                        int jarg2)

RNAstructureBackendCalculator_getTurboFoldSequenceSetData

public static final java.lang.String RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long jarg1,
                                                                                               RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_getVersion

public static final java.lang.String RNAstructureBackendCalculator_getVersion()

RNAstructureBackendCalculator_loadDoubleRNA__SWIG_0

public static final java.lang.String RNAstructureBackendCalculator_loadDoubleRNA__SWIG_0(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_,
                                                                                         java.lang.String jarg2,
                                                                                         java.lang.String jarg3,
                                                                                         boolean jarg4,
                                                                                         int jarg5)

RNAstructureBackendCalculator_loadDoubleRNA__SWIG_1

public static final java.lang.String RNAstructureBackendCalculator_loadDoubleRNA__SWIG_1(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_,
                                                                                         java.lang.String jarg2,
                                                                                         java.lang.String jarg3,
                                                                                         boolean jarg4)

RNAstructureBackendCalculator_loadSingleRNA__SWIG_0

public static final java.lang.String RNAstructureBackendCalculator_loadSingleRNA__SWIG_0(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_,
                                                                                         java.lang.String jarg2,
                                                                                         boolean jarg3,
                                                                                         int jarg4)

RNAstructureBackendCalculator_loadSingleRNA__SWIG_1

public static final java.lang.String RNAstructureBackendCalculator_loadSingleRNA__SWIG_1(long jarg1,
                                                                                         RNAstructureBackendCalculator jarg1_,
                                                                                         java.lang.String jarg2,
                                                                                         boolean jarg3)

RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile

public static final java.lang.String RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long jarg1,
                                                                                                        RNAstructureBackendCalculator jarg1_,
                                                                                                        java.lang.String jarg2)

RNAstructureBackendCalculator_readFoldingConstraintsFile

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

RNAstructureBackendCalculator_readSequenceData

public static final void RNAstructureBackendCalculator_readSequenceData(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_,
                                                                        java.lang.String jarg2)

RNAstructureBackendCalculator_runAccessFold

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

RNAstructureBackendCalculator_runAllSub

public static final java.lang.String RNAstructureBackendCalculator_runAllSub(long jarg1,
                                                                             RNAstructureBackendCalculator jarg1_,
                                                                             java.lang.String jarg2,
                                                                             float jarg3,
                                                                             double jarg4)

RNAstructureBackendCalculator_runBifold

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

RNAstructureBackendCalculator_runBipartition

public static final java.lang.String RNAstructureBackendCalculator_runBipartition(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  java.lang.String jarg2)

RNAstructureBackendCalculator_runDuplexFold

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

RNAstructureBackendCalculator_runDynalign

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

RNAstructureBackendCalculator_runDynalignRefold

public static final java.lang.String RNAstructureBackendCalculator_runDynalignRefold(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_,
                                                                                     java.lang.String jarg2,
                                                                                     java.lang.String jarg3,
                                                                                     java.lang.String jarg4,
                                                                                     int jarg5,
                                                                                     int jarg6,
                                                                                     int jarg7,
                                                                                     int jarg8)

RNAstructureBackendCalculator_runEfn2

public static final java.lang.String RNAstructureBackendCalculator_runEfn2(long jarg1,
                                                                           RNAstructureBackendCalculator jarg1_,
                                                                           java.lang.String jarg2,
                                                                           boolean jarg3)

RNAstructureBackendCalculator_runFold

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

RNAstructureBackendCalculator_runMaxExpect

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

RNAstructureBackendCalculator_runMultilign

public static final java.lang.String RNAstructureBackendCalculator_runMultilign(long jarg1,
                                                                                RNAstructureBackendCalculator jarg1_,
                                                                                int jarg2,
                                                                                int jarg3,
                                                                                int jarg4,
                                                                                int jarg5,
                                                                                double jarg6,
                                                                                boolean jarg7,
                                                                                double jarg8,
                                                                                int jarg9,
                                                                                int jarg10,
                                                                                java.lang.String jarg11,
                                                                                boolean jarg12,
                                                                                boolean jarg13)

RNAstructureBackendCalculator_runOligoScreen

public static final java.lang.String RNAstructureBackendCalculator_runOligoScreen(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  java.lang.String jarg2,
                                                                                  java.lang.String jarg3,
                                                                                  boolean jarg4)

RNAstructureBackendCalculator_runOligoWalk

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

RNAstructureBackendCalculator_runPartition

public static final java.lang.String RNAstructureBackendCalculator_runPartition(long jarg1,
                                                                                RNAstructureBackendCalculator jarg1_,
                                                                                java.lang.String jarg2)

RNAstructureBackendCalculator_runPseudoknotPrediction

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

RNAstructureBackendCalculator_runPseudoknotRemoval

public static final java.lang.String RNAstructureBackendCalculator_runPseudoknotRemoval(long jarg1,
                                                                                        RNAstructureBackendCalculator jarg1_,
                                                                                        java.lang.String jarg2,
                                                                                        boolean jarg3)

RNAstructureBackendCalculator_runRefold

public static final java.lang.String RNAstructureBackendCalculator_runRefold(long jarg1,
                                                                             RNAstructureBackendCalculator jarg1_,
                                                                             java.lang.String jarg2,
                                                                             int jarg3,
                                                                             int jarg4,
                                                                             int jarg5)

RNAstructureBackendCalculator_runStochastic

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

RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_0

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_0(long jarg1,
                                                                                                               RNAstructureBackendCalculator jarg1_,
                                                                                                               double jarg2,
                                                                                                               int jarg3,
                                                                                                               double jarg4,
                                                                                                               int jarg5,
                                                                                                               int jarg6,
                                                                                                               double jarg7,
                                                                                                               java.lang.String jarg8)

RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_1

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_1(long jarg1,
                                                                                                               RNAstructureBackendCalculator jarg1_,
                                                                                                               double jarg2,
                                                                                                               int jarg3,
                                                                                                               double jarg4,
                                                                                                               int jarg5,
                                                                                                               int jarg6,
                                                                                                               double jarg7)

RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_0

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_0(long jarg1,
                                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                                  double jarg2,
                                                                                                  int jarg3,
                                                                                                  int jarg4,
                                                                                                  int jarg5,
                                                                                                  java.lang.String jarg6)

RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_1

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_1(long jarg1,
                                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                                  double jarg2,
                                                                                                  int jarg3,
                                                                                                  int jarg4,
                                                                                                  int jarg5)

RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_0

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_0(long jarg1,
                                                                                                 RNAstructureBackendCalculator jarg1_,
                                                                                                 double jarg2,
                                                                                                 int jarg3,
                                                                                                 double jarg4,
                                                                                                 java.lang.String jarg5)

RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_1

public static final java.lang.String RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_1(long jarg1,
                                                                                                 RNAstructureBackendCalculator jarg1_,
                                                                                                 double jarg2,
                                                                                                 int jarg3,
                                                                                                 double jarg4)

RNAstructureBackendCalculator_setCleavedNucleotide

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

RNAstructureBackendCalculator_setDoubleStrandedNucleotide

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

RNAstructureBackendCalculator_setDynalignAlignmentConstraint

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

RNAstructureBackendCalculator_setEnvVar

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

RNAstructureBackendCalculator_setForcedHelix

public static final java.lang.String RNAstructureBackendCalculator_setForcedHelix(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  int jarg2,
                                                                                  int jarg3,
                                                                                  int jarg4,
                                                                                  int jarg5)

RNAstructureBackendCalculator_setMaxLoop

public static final void RNAstructureBackendCalculator_setMaxLoop(long jarg1,
                                                                  RNAstructureBackendCalculator jarg1_,
                                                                  int jarg2)

RNAstructureBackendCalculator_setMaxPair

public static final void RNAstructureBackendCalculator_setMaxPair(long jarg1,
                                                                  RNAstructureBackendCalculator jarg1_,
                                                                  int jarg2)

RNAstructureBackendCalculator_setModifiedNucleotide

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

RNAstructureBackendCalculator_setProhibitedHelix

public static final java.lang.String RNAstructureBackendCalculator_setProhibitedHelix(long jarg1,
                                                                                      RNAstructureBackendCalculator jarg1_,
                                                                                      int jarg2,
                                                                                      int jarg3,
                                                                                      int jarg4,
                                                                                      int jarg5)

RNAstructureBackendCalculator_setSaveFile

public static final void RNAstructureBackendCalculator_setSaveFile(long jarg1,
                                                                   RNAstructureBackendCalculator jarg1_,
                                                                   java.lang.String jarg2)

RNAstructureBackendCalculator_setSequenceComment

public static final void RNAstructureBackendCalculator_setSequenceComment(long jarg1,
                                                                          RNAstructureBackendCalculator jarg1_,
                                                                          java.lang.String jarg2)

RNAstructureBackendCalculator_setSequenceData

public static final void RNAstructureBackendCalculator_setSequenceData(long jarg1,
                                                                       RNAstructureBackendCalculator jarg1_,
                                                                       java.lang.String jarg2)

RNAstructureBackendCalculator_setSequenceTitle

public static final void RNAstructureBackendCalculator_setSequenceTitle(long jarg1,
                                                                        RNAstructureBackendCalculator jarg1_,
                                                                        java.lang.String jarg2)

RNAstructureBackendCalculator_setSHAPEFile

public static final void RNAstructureBackendCalculator_setSHAPEFile(long jarg1,
                                                                    RNAstructureBackendCalculator jarg1_,
                                                                    java.lang.String jarg2)

RNAstructureBackendCalculator_setSHAPEParam1

public static final void RNAstructureBackendCalculator_setSHAPEParam1(long jarg1,
                                                                      RNAstructureBackendCalculator jarg1_,
                                                                      double jarg2)

RNAstructureBackendCalculator_setSHAPEParam2

public static final void RNAstructureBackendCalculator_setSHAPEParam2(long jarg1,
                                                                      RNAstructureBackendCalculator jarg1_,
                                                                      double jarg2)

RNAstructureBackendCalculator_setSHAPEType

public static final void RNAstructureBackendCalculator_setSHAPEType(long jarg1,
                                                                    RNAstructureBackendCalculator jarg1_,
                                                                    boolean jarg2)

RNAstructureBackendCalculator_setSingleStrandedNucleotide

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

RNAstructureBackendCalculator_setTemperature

public static final void RNAstructureBackendCalculator_setTemperature(long jarg1,
                                                                      RNAstructureBackendCalculator jarg1_,
                                                                      double jarg2)

RNAstructureBackendCalculator_wasCanceled

public static final boolean RNAstructureBackendCalculator_wasCanceled(long jarg1,
                                                                      RNAstructureBackendCalculator jarg1_)

RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile

public static final void RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long jarg1,
                                                                                             RNAstructureBackendCalculator jarg1_,
                                                                                             java.lang.String jarg2)

RNAstructureBackendCalculator_writeFastaFile

public static final java.lang.String RNAstructureBackendCalculator_writeFastaFile(long jarg1,
                                                                                  RNAstructureBackendCalculator jarg1_,
                                                                                  java.lang.String jarg2)

RNAstructureBackendCalculator_writeFoldingConstraintsFile

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

RNAstructureBackendCalculator_writeSequenceFile

public static final java.lang.String RNAstructureBackendCalculator_writeSequenceFile(long jarg1,
                                                                                     RNAstructureBackendCalculator jarg1_,
                                                                                     java.lang.String jarg2)