RNAstructure_java_interface.source.startup

## Class RNAstructureBackendCalculatorProxyJNI

- java.lang.Object
- - RNAstructure_java_interface.source.startup.RNAstructureBackendCalculatorProxyJNI

     class RNAstructureBackendCalculatorProxyJNI
    extends Object

### Constructor Summary

Constructors
Constructor and Description
`RNAstructureBackendCalculatorProxyJNI()`

### Method Summary

Methods
`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_, String jarg2, String jarg3)`
`static void` `RNAstructureBackendCalculator_addTurboFoldTuple(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3)`
`static String` `RNAstructureBackendCalculator_buildAllSubDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildBifoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4)`
`static String` `RNAstructureBackendCalculator_buildBipartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4)`
`static String` `RNAstructureBackendCalculator_buildDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4)`
`static String` `RNAstructureBackendCalculator_buildEfn2DataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildFoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildMaxExpectDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_buildOligoScreenDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_buildOligoWalkDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildPartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildProbKnotDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_buildStochasticDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`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_, String jarg2, int jarg3, boolean jarg4, boolean jarg5, String jarg6)`
`static String` `RNAstructureBackendCalculator_getAllOligoData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static String` `RNAstructureBackendCalculator_getDisplayedOligo(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static String` `RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getDynalignStructureWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getFoldingConstraints(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static int` `RNAstructureBackendCalculator_getFoldWindowSize(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 String` `RNAstructureBackendCalculator_getMultilignCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static int` `RNAstructureBackendCalculator_getMultilignMaxPairs(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getMultilignSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getNumMultilignSequences(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getNumTurboFoldSequences(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getOligoLabelData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static int` `RNAstructureBackendCalculator_getOligoTargetLength(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getOligoTargetSequence(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getProgressNumber(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static int` `RNAstructureBackendCalculator_getRefoldWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_getSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static 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 String` `RNAstructureBackendCalculator_getTurboFoldCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static String` `RNAstructureBackendCalculator_getTurboFoldSaveFile(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2)`
`static String` `RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_)`
`static String` `RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_readFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3)`
`static void` `RNAstructureBackendCalculator_readSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_runAllSub(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, float jarg3, double jarg4)`
`static String` `RNAstructureBackendCalculator_runBifold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, float jarg3, int jarg4, int jarg5, boolean jarg6, boolean jarg7)`
`static String` `RNAstructureBackendCalculator_runBipartition(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_runDynalign(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, String jarg4, String jarg5, double jarg6, int jarg7, int jarg8, int jarg9, float jarg10, boolean jarg11)`
`static String` `RNAstructureBackendCalculator_runDynalignRefold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, String jarg4, int jarg5, int jarg6, int jarg7, int jarg8)`
`static String` `RNAstructureBackendCalculator_runEfn2(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_runFold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4, int jarg5, boolean jarg6)`
`static String` `RNAstructureBackendCalculator_runMaxExpect(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, double jarg3, int jarg4, int jarg5, double jarg6)`
`static 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, String jarg11, boolean jarg12, boolean jarg13)`
`static String` `RNAstructureBackendCalculator_runOligoScreen(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4)`
`static String` `RNAstructureBackendCalculator_runOligoWalk(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, String jarg4, boolean jarg5, int jarg6, int jarg7, String jarg8, int jarg9, int jarg10)`
`static String` `RNAstructureBackendCalculator_runPartition(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_runPseudoknotPrediction(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4)`
`static String` `RNAstructureBackendCalculator_runPseudoknotRemoval(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3)`
`static String` `RNAstructureBackendCalculator_runRefold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4, int jarg5)`
`static String` `RNAstructureBackendCalculator_runStochastic(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4)`
`static String` `RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4, int jarg5, int jarg6, double jarg7)`
`static String` `RNAstructureBackendCalculator_runTurboFoldPseudoknot(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, int jarg4, int jarg5)`
`static String` `RNAstructureBackendCalculator_runTurboFoldThreshold(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4)`
`static String` `RNAstructureBackendCalculator_setCleavedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)`
`static String` `RNAstructureBackendCalculator_setDoubleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)`
`static String` `RNAstructureBackendCalculator_setDynalignAlignmentConstraint(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)`
`static 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 String` `RNAstructureBackendCalculator_setModifiedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)`
`static String` `RNAstructureBackendCalculator_setProhibitedHelix(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5)`
`static void` `RNAstructureBackendCalculator_setSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static void` `RNAstructureBackendCalculator_setSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static void` `RNAstructureBackendCalculator_setSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static void` `RNAstructureBackendCalculator_setSHAPEFile(long jarg1, RNAstructureBackendCalculator jarg1_, 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 String` `RNAstructureBackendCalculator_setSingleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3)`
`static void` `RNAstructureBackendCalculator_setTemperature(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2)`
`static void` `RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_writeFastaFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`
`static String` `RNAstructureBackendCalculator_writeFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3)`
`static String` `RNAstructureBackendCalculator_writeSequenceFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2)`

### Methods inherited from class java.lang.Object

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

### Constructor Detail

#### RNAstructureBackendCalculatorProxyJNI

    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_,
                                                       String jarg2,
                                                       String jarg3)

#### RNAstructureBackendCalculator_addTurboFoldTuple

    public static final void RNAstructureBackendCalculator_addTurboFoldTuple(long jarg1,
                                                       RNAstructureBackendCalculator jarg1_,
                                                       String jarg2,
                                                       String jarg3)

#### RNAstructureBackendCalculator_buildAllSubDataStructure

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

#### RNAstructureBackendCalculator_buildBifoldDataStructure

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

#### RNAstructureBackendCalculator_buildBipartitionDataStructure

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

#### RNAstructureBackendCalculator_buildDynalignDataStructure

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

#### RNAstructureBackendCalculator_buildEfn2DataStructure

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

#### RNAstructureBackendCalculator_buildFoldDataStructure

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

#### RNAstructureBackendCalculator_buildMaxExpectDataStructure

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

#### RNAstructureBackendCalculator_buildOligoScreenDataStructure

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

#### RNAstructureBackendCalculator_buildOligoWalkDataStructure

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

#### RNAstructureBackendCalculator_buildPartitionDataStructure

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

#### RNAstructureBackendCalculator_buildProbKnotDataStructure

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

#### RNAstructureBackendCalculator_buildRefoldDynalignDataStructure

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

#### RNAstructureBackendCalculator_buildRefoldSingleDataStructure

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

#### RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure

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

#### RNAstructureBackendCalculator_buildStochasticDataStructure

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

#### 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_,
                                               String jarg2,
                                               int jarg3,
                                               boolean jarg4,
                                               boolean jarg5,
                                               String jarg6)

#### RNAstructureBackendCalculator_getAllOligoData

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

#### RNAstructureBackendCalculator_getDisplayedOligo

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

#### RNAstructureBackendCalculator_getDynalignAlignmentConstraints

    public static final 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_getFoldingConstraints

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

#### RNAstructureBackendCalculator_getFoldWindowSize

    public static final int RNAstructureBackendCalculator_getFoldWindowSize(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 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 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 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 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_getSequenceComment

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

#### RNAstructureBackendCalculator_getSequenceData

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

#### RNAstructureBackendCalculator_getSequenceTitle

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

#### RNAstructureBackendCalculator_getStructureType

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

#### RNAstructureBackendCalculator_getTurboFoldSaveFile

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

#### RNAstructureBackendCalculator_getTurboFoldSequenceSetData

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

#### RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile

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

#### RNAstructureBackendCalculator_readFoldingConstraintsFile

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

#### RNAstructureBackendCalculator_readSequenceData

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

#### RNAstructureBackendCalculator_runAllSub

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

#### RNAstructureBackendCalculator_runBifold

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

#### RNAstructureBackendCalculator_runBipartition

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

#### RNAstructureBackendCalculator_runDynalign

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

#### RNAstructureBackendCalculator_runDynalignRefold

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

#### RNAstructureBackendCalculator_runEfn2

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

#### RNAstructureBackendCalculator_runFold

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

#### RNAstructureBackendCalculator_runMaxExpect

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

#### RNAstructureBackendCalculator_runMultilign

    public static final 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,
                                                    String jarg11,
                                                    boolean jarg12,
                                                    boolean jarg13)

#### RNAstructureBackendCalculator_runOligoScreen

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

#### RNAstructureBackendCalculator_runOligoWalk

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

#### RNAstructureBackendCalculator_runPartition

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

#### RNAstructureBackendCalculator_runPseudoknotPrediction

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

#### RNAstructureBackendCalculator_runPseudoknotRemoval

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

#### RNAstructureBackendCalculator_runRefold

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

#### RNAstructureBackendCalculator_runStochastic

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

#### RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy

    public static final String RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy(long jarg1,
                                                                           RNAstructureBackendCalculator jarg1_,
                                                                           double jarg2,
                                                                           int jarg3,
                                                                           double jarg4,
                                                                           int jarg5,
                                                                           int jarg6,
                                                                           double jarg7)

#### RNAstructureBackendCalculator_runTurboFoldPseudoknot

    public static final String RNAstructureBackendCalculator_runTurboFoldPseudoknot(long jarg1,
                                                              RNAstructureBackendCalculator jarg1_,
                                                              double jarg2,
                                                              int jarg3,
                                                              int jarg4,
                                                              int jarg5)

#### RNAstructureBackendCalculator_runTurboFoldThreshold

    public static final String RNAstructureBackendCalculator_runTurboFoldThreshold(long jarg1,
                                                             RNAstructureBackendCalculator jarg1_,
                                                             double jarg2,
                                                             int jarg3,
                                                             double jarg4)

#### RNAstructureBackendCalculator_setCleavedNucleotide

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

#### RNAstructureBackendCalculator_setDoubleStrandedNucleotide

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

#### RNAstructureBackendCalculator_setDynalignAlignmentConstraint

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

#### RNAstructureBackendCalculator_setForcedHelix

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

#### RNAstructureBackendCalculator_setProhibitedHelix

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

#### RNAstructureBackendCalculator_setSequenceComment

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

#### RNAstructureBackendCalculator_setSequenceData

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

#### RNAstructureBackendCalculator_setSequenceTitle

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

#### RNAstructureBackendCalculator_setSHAPEFile

    public static final void RNAstructureBackendCalculator_setSHAPEFile(long jarg1,
                                                  RNAstructureBackendCalculator jarg1_,
                                                  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 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_writeDynalignAlignmentConstraintsFile

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

#### RNAstructureBackendCalculator_writeFastaFile

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

#### RNAstructureBackendCalculator_writeFoldingConstraintsFile

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

#### RNAstructureBackendCalculator_writeSequenceFile

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