/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 1.3.40
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

package RNAstructure_java_interface.source.startup;

class RNAstructureBackendCalculatorProxyJNI {
  public final static native long new_RNAstructureBackendCalculator();
  public final static native void delete_RNAstructureBackendCalculator(long jarg1);
  public final static native String RNAstructureBackendCalculator_buildAllSubDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native double RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native float RNAstructureBackendCalculator_getSuboptimalPercentDiff(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_runAllSub(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, float jarg3, double jarg4);
  public final static native String RNAstructureBackendCalculator_buildBifoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4);
  public final static native String RNAstructureBackendCalculator_runBifold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, float jarg3, int jarg4, int jarg5, boolean jarg6, boolean jarg7);
  public final static native String RNAstructureBackendCalculator_buildBipartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4);
  public final static native String RNAstructureBackendCalculator_runBipartition(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_buildDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4);
  public final static native void RNAstructureBackendCalculator_clearDynalignAlignmentConstraints(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getDynalignStructureWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native 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);
  public final static native String RNAstructureBackendCalculator_setDynalignAlignmentConstraint(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3);
  public final static native void RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_buildEfn2DataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native String RNAstructureBackendCalculator_runEfn2(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native String RNAstructureBackendCalculator_buildFoldDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native int RNAstructureBackendCalculator_getFoldWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_runFold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4, int jarg5, boolean jarg6);
  public final static native String RNAstructureBackendCalculator_buildMaxExpectDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_runMaxExpect(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, double jarg3, int jarg4, int jarg5, double jarg6);
  public final static native void RNAstructureBackendCalculator_activateMultilign(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native void RNAstructureBackendCalculator_addMultilignTuple(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3);
  public final static native void RNAstructureBackendCalculator_deleteMultilignTuple(long jarg1, RNAstructureBackendCalculator jarg1_, long jarg2);
  public final static native String RNAstructureBackendCalculator_getMultilignCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_getMultilignMaxPairs(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getMultilignSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getNumMultilignSequences(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native 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);
  public final static native String RNAstructureBackendCalculator_buildOligoScreenDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_runOligoScreen(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, boolean jarg4);
  public final static native String RNAstructureBackendCalculator_buildOligoWalkDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native boolean RNAstructureBackendCalculator_canFoldOligoOligo(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native boolean RNAstructureBackendCalculator_canFoldOligoSelf(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_determineOligoMaximum(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native void RNAstructureBackendCalculator_foldOligo(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, boolean jarg4, boolean jarg5, String jarg6);
  public final static native String RNAstructureBackendCalculator_getAllOligoData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native String RNAstructureBackendCalculator_getDisplayedOligo(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_getGraphRegionBegin(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getGraphRegionEnd(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getMostStableOligo(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getOligoLabelData(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_getOligoTargetLength(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getOligoTargetSequence(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native 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);
  public final static native String RNAstructureBackendCalculator_buildPartitionDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native String RNAstructureBackendCalculator_runPartition(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_buildProbKnotDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_runPseudoknotPrediction(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4);
  public final static native String RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_runDynalignRefold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3, String jarg4, int jarg5, int jarg6, int jarg7, int jarg8);
  public final static native String RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native int RNAstructureBackendCalculator_getRefoldWindowSize(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_runRefold(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4, int jarg5);
  public final static native String RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native String RNAstructureBackendCalculator_runPseudoknotRemoval(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, boolean jarg3);
  public final static native String RNAstructureBackendCalculator_getSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native void RNAstructureBackendCalculator_readSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native void RNAstructureBackendCalculator_setSequenceComment(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native void RNAstructureBackendCalculator_setSequenceData(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native void RNAstructureBackendCalculator_setSequenceTitle(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_writeFastaFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_writeSequenceFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_buildStochasticDataStructure(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native String RNAstructureBackendCalculator_runStochastic(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3, int jarg4);
  public final static native void RNAstructureBackendCalculator_activateTurboFold(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native void RNAstructureBackendCalculator_addTurboFoldTuple(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, String jarg3);
  public final static native void RNAstructureBackendCalculator_deleteTurboFoldTuple(long jarg1, RNAstructureBackendCalculator jarg1_, long jarg2);
  public final static native int RNAstructureBackendCalculator_getNumTurboFoldSequences(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getTurboFoldCT(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native String RNAstructureBackendCalculator_getTurboFoldSaveFile(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native String RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4, int jarg5, int jarg6, double jarg7);
  public final static native String RNAstructureBackendCalculator_runTurboFoldPseudoknot(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, int jarg4, int jarg5);
  public final static native String RNAstructureBackendCalculator_runTurboFoldThreshold(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2, int jarg3, double jarg4);
  public final static native void RNAstructureBackendCalculator_clearFoldingConstraints(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native String RNAstructureBackendCalculator_getFoldingConstraints(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_getMaxConstraintIndex(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native int RNAstructureBackendCalculator_getMaxLoop(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native int RNAstructureBackendCalculator_getMaxPair(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native double RNAstructureBackendCalculator_getTemperature(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_readFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3);
  public final static native String RNAstructureBackendCalculator_setCleavedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3);
  public final static native String RNAstructureBackendCalculator_setDoubleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3);
  public final static native String RNAstructureBackendCalculator_setForcedHelix(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5);
  public final static native void RNAstructureBackendCalculator_setMaxLoop(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native void RNAstructureBackendCalculator_setMaxPair(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2);
  public final static native String RNAstructureBackendCalculator_setModifiedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3);
  public final static native String RNAstructureBackendCalculator_setProhibitedHelix(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3, int jarg4, int jarg5);
  public final static native void RNAstructureBackendCalculator_setSHAPEFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2);
  public final static native void RNAstructureBackendCalculator_setSHAPEParam1(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2);
  public final static native void RNAstructureBackendCalculator_setSHAPEParam2(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2);
  public final static native void RNAstructureBackendCalculator_setSHAPEType(long jarg1, RNAstructureBackendCalculator jarg1_, boolean jarg2);
  public final static native String RNAstructureBackendCalculator_setSingleStrandedNucleotide(long jarg1, RNAstructureBackendCalculator jarg1_, int jarg2, int jarg3);
  public final static native void RNAstructureBackendCalculator_setTemperature(long jarg1, RNAstructureBackendCalculator jarg1_, double jarg2);
  public final static native String RNAstructureBackendCalculator_writeFoldingConstraintsFile(long jarg1, RNAstructureBackendCalculator jarg1_, String jarg2, int jarg3);
  public final static native int RNAstructureBackendCalculator_getProgressNumber(long jarg1, RNAstructureBackendCalculator jarg1_);
  public final static native String RNAstructureBackendCalculator_getStructureType(long jarg1, RNAstructureBackendCalculator jarg1_);
}
