RNAstructure_java_interface.source.startup

## Class RNAstructureBackendCalculator

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

    public class RNAstructureBackendCalculator
    extends Object

### Field Summary

Fields
`protected boolean` `swigCMemOwn`
`private long` `swigCPtr`

### Constructor Summary

Constructors
`` `RNAstructureBackendCalculator()`
`protected` `RNAstructureBackendCalculator(long cPtr, boolean cMemoryOwn)`

### Method Summary

Methods
`void` `activateMultilign()`
`void` `activateTurboFold()`
`void` `addMultilignTuple(String seqFile, String ctFile)`
`void` `addTurboFoldTuple(String seqFile, String ctFile)`
`String` `buildAllSubDataStructure(String file, boolean isRNA)`
`String` `buildBifoldDataStructure(String file1, String file2, boolean isRNA)`
`String` `buildBipartitionDataStructure(String file1, String file2, boolean isRNA)`
`String` `buildDynalignDataStructure(String file1, String file2, boolean isRNA)`
`String` `buildEfn2DataStructure(String file, boolean isRNA)`
`String` `buildFoldDataStructure(String file, boolean isRNA)`
`String` `buildMaxExpectDataStructure(String file)`
`String` `buildOligoScreenDataStructure()`
`String` `buildOligoWalkDataStructure(String file, boolean isRNA)`
`String` `buildPartitionDataStructure(String file, boolean isRNA)`
`String` `buildProbKnotDataStructure(String file)`
`String` `buildRefoldDynalignDataStructure(String file)`
`String` `buildRefoldSingleDataStructure(String file)`
`String` `buildRemovePseudoknotsDataStructure(String file, boolean isRNA)`
`String` `buildStochasticDataStructure(String file)`
`boolean` `canFoldOligoOligo(int index)`
`boolean` `canFoldOligoSelf(int index)`
`void` `clearDynalignAlignmentConstraints()`
`void` `clearFoldingConstraints(int strand)`
`void` `delete()`
`void` `deleteMultilignTuple(long index)`
`void` `deleteTurboFoldTuple(long index)`
`int` `determineOligoMaximum(int length)`
`protected void` `finalize()`
`void` `foldOligo(String sequence, int index, boolean bimolecular, boolean isRNA, String file)`
`String` `getAllOligoData(int height)`
`protected static long` `getCPtr(RNAstructureBackendCalculator obj)`
`String` `getDisplayedOligo(int index)`
`String` `getDynalignAlignmentConstraints()`
`int` `getDynalignAlignmentWindowSize()`
`int` `getDynalignStructureWindowSize()`
`String` `getFoldingConstraints(int strand)`
`int` `getFoldWindowSize()`
`int` `getGraphRegionBegin()`
`int` `getGraphRegionEnd()`
`int` `getMaxConstraintIndex(int strand)`
`int` `getMaxLoop()`
`int` `getMaxPair()`
`int` `getMostStableOligo()`
`String` `getMultilignCT(int index)`
`int` `getMultilignMaxPairs()`
`String` `getMultilignSequenceSetData()`
`int` `getNumMultilignSequences()`
`int` `getNumTurboFoldSequences()`
`String` `getOligoLabelData(int index)`
`int` `getOligoTargetLength()`
`String` `getOligoTargetSequence()`
`int` `getProgressNumber()`
`int` `getRefoldWindowSize()`
`String` `getSequenceComment()`
`String` `getSequenceData()`
`String` `getSequenceTitle()`
`String` `getStructureType()`
`double` `getSuboptimalAbsoluteDiff()`
`float` `getSuboptimalPercentDiff()`
`double` `getTemperature()`
`String` `getTurboFoldCT(int index)`
`String` `getTurboFoldSaveFile(int index)`
`String` `getTurboFoldSequenceSetData()`
`String` `readDynalignAlignmentConstraintsFile(String file)`
`String` `readFoldingConstraintsFile(String file, int strand)`
`void` `readSequenceData(String file)`
`String` `runAllSub(String ct, float percent, double absolute)`
`String` `runBifold(String ctFile, float percent, int maxStructures, int windowSize, boolean saveFile, boolean intraForbidden)`
`String` `runBipartition(String pfsFile)`
`String` `runDynalign(String ctFile1, String ctFile2, String saveFile, String alignFile, double percent, int structures, int windowStr, int windowAli, float gap, boolean isInsert)`
`String` `runDynalignRefold(String ctFile1, String ctFile2, String alignFile, int percent, int structures, int windowStr, int windowAli)`
`String` `runEfn2(String outFile, boolean writeDetails)`
`String` `runFold(String ctFile, int percent, int structures, int window, boolean save)`
`String` `runMaxExpect(String ctFile, double score, int structures, int window, double gamma)`
`String` `runMultilign(int percent, int maxStructures, int bpWindow, int alignWindow, double gap, boolean insert, double maxDsvChange, int maxPairs, int cycles, String alignFile, boolean saveFiles, boolean isRNA)`
`String` `runOligoScreen(String in, String out, boolean isRNA)`
`String` `runOligoWalk(String report, int mode, String chemistry, boolean suboptimal, int length, int amount, String unit, int start, int stop)`
`String` `runPartition(String pfsFile)`
`String` `runPseudoknotPrediction(String ctFile, int iterations, int helix)`
`String` `runPseudoknotRemoval(String ctFile, boolean minimize)`
`String` `runRefold(String ctFile, int percent, int structures, int window)`
`String` `runStochastic(String outFile, int ensemble, int seed)`
`String` `runTurboFoldMaximumExpectedAccuracy(double turboGamma, int turboIterations, double percent, int structures, int window, double meaGamma)`
`String` `runTurboFoldPseudoknot(double turboGamma, int turboIterations, int pkIterations, int helix)`
`String` `runTurboFoldThreshold(double turboGamma, int turboIterations, double threshold)`
`String` `setCleavedNucleotide(int nuc, int strand)`
`String` `setDoubleStrandedNucleotide(int nuc, int strand)`
`String` `setDynalignAlignmentConstraint(int nuc1, int nuc2)`
`String` `setForcedHelix(int nuc1, int nuc2, int length, int strand)`
`void` `setMaxLoop(int newLoop)`
`void` `setMaxPair(int newPair)`
`String` `setModifiedNucleotide(int nuc, int strand)`
`String` `setProhibitedHelix(int nuc1, int nuc2, int length, int strand)`
`void` `setSequenceComment(String comment)`
`void` `setSequenceData(String data)`
`void` `setSequenceTitle(String title)`
`void` `setSHAPEFile(String file)`
`void` `setSHAPEParam1(double value)`
`void` `setSHAPEParam2(double value)`
`void` `setSHAPEType(boolean isEnergy)`
`String` `setSingleStrandedNucleotide(int nuc, int strand)`
`void` `setTemperature(double newTemp)`
`void` `writeDynalignAlignmentConstraintsFile(String file)`
`String` `writeFastaFile(String file)`
`String` `writeFoldingConstraintsFile(String file, int strand)`
`String` `writeSequenceFile(String file)`

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

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

### Field Detail

#### swigCMemOwn

    protected boolean swigCMemOwn

#### swigCPtr

    private long swigCPtr

### Constructor Detail

#### RNAstructureBackendCalculator

    public RNAstructureBackendCalculator()

#### RNAstructureBackendCalculator

    protected RNAstructureBackendCalculator(long cPtr,
                                 boolean cMemoryOwn)

### Method Detail

#### activateMultilign

    public void activateMultilign()

#### activateTurboFold

    public void activateTurboFold()

#### addMultilignTuple

    public void addMultilignTuple(String seqFile,
                         String ctFile)

#### addTurboFoldTuple

    public void addTurboFoldTuple(String seqFile,
                         String ctFile)

#### buildAllSubDataStructure

    public String buildAllSubDataStructure(String file,
                                  boolean isRNA)

#### buildBifoldDataStructure

    public String buildBifoldDataStructure(String file1,
                                  String file2,
                                  boolean isRNA)

#### buildBipartitionDataStructure

    public String buildBipartitionDataStructure(String file1,
                                       String file2,
                                       boolean isRNA)

#### buildDynalignDataStructure

    public String buildDynalignDataStructure(String file1,
                                    String file2,
                                    boolean isRNA)

#### buildEfn2DataStructure

    public String buildEfn2DataStructure(String file,
                                boolean isRNA)

#### buildFoldDataStructure

    public String buildFoldDataStructure(String file,
                                boolean isRNA)

#### buildMaxExpectDataStructure

    public String buildMaxExpectDataStructure(String file)

#### buildOligoScreenDataStructure

    public String buildOligoScreenDataStructure()

#### buildOligoWalkDataStructure

    public String buildOligoWalkDataStructure(String file,
                                     boolean isRNA)

#### buildPartitionDataStructure

    public String buildPartitionDataStructure(String file,
                                     boolean isRNA)

#### buildProbKnotDataStructure

    public String buildProbKnotDataStructure(String file)

#### buildRefoldDynalignDataStructure

    public String buildRefoldDynalignDataStructure(String file)

#### buildRefoldSingleDataStructure

    public String buildRefoldSingleDataStructure(String file)

#### buildRemovePseudoknotsDataStructure

    public String buildRemovePseudoknotsDataStructure(String file,
                                             boolean isRNA)

#### buildStochasticDataStructure

    public String buildStochasticDataStructure(String file)

#### canFoldOligoOligo

    public boolean canFoldOligoOligo(int index)

#### canFoldOligoSelf

    public boolean canFoldOligoSelf(int index)

#### clearDynalignAlignmentConstraints

    public void clearDynalignAlignmentConstraints()

#### clearFoldingConstraints

    public void clearFoldingConstraints(int strand)

#### delete

    public void delete()

#### deleteMultilignTuple

    public void deleteMultilignTuple(long index)

#### deleteTurboFoldTuple

    public void deleteTurboFoldTuple(long index)

#### determineOligoMaximum

    public int determineOligoMaximum(int length)

#### finalize

    protected void finalize()

Overrides:
  `finalize` in class `Object`

#### foldOligo

    public void foldOligo(String sequence,
                 int index,
                 boolean bimolecular,
                 boolean isRNA,
                 String file)

#### getAllOligoData

    public String getAllOligoData(int height)

#### getCPtr

    protected static long getCPtr(RNAstructureBackendCalculator obj)

#### getDisplayedOligo

    public String getDisplayedOligo(int index)

#### getDynalignAlignmentConstraints

    public String getDynalignAlignmentConstraints()

#### getDynalignAlignmentWindowSize

    public int getDynalignAlignmentWindowSize()

#### getDynalignStructureWindowSize

    public int getDynalignStructureWindowSize()

#### getFoldingConstraints

    public String getFoldingConstraints(int strand)

#### getFoldWindowSize

    public int getFoldWindowSize()

#### getGraphRegionBegin

    public int getGraphRegionBegin()

#### getGraphRegionEnd

    public int getGraphRegionEnd()

#### getMaxConstraintIndex

    public int getMaxConstraintIndex(int strand)

#### getMaxLoop

    public int getMaxLoop()

#### getMaxPair

    public int getMaxPair()

#### getMostStableOligo

    public int getMostStableOligo()

#### getMultilignCT

    public String getMultilignCT(int index)

#### getMultilignMaxPairs

    public int getMultilignMaxPairs()

#### getMultilignSequenceSetData

    public String getMultilignSequenceSetData()

#### getNumMultilignSequences

    public int getNumMultilignSequences()

#### getNumTurboFoldSequences

    public int getNumTurboFoldSequences()

#### getOligoLabelData

    public String getOligoLabelData(int index)

#### getOligoTargetLength

    public int getOligoTargetLength()

#### getOligoTargetSequence

    public String getOligoTargetSequence()

#### getProgressNumber

    public int getProgressNumber()

#### getRefoldWindowSize

    public int getRefoldWindowSize()

#### getSequenceComment

    public String getSequenceComment()

#### getSequenceData

    public String getSequenceData()

#### getSequenceTitle

    public String getSequenceTitle()

#### getStructureType

    public String getStructureType()

#### getSuboptimalAbsoluteDiff

    public double getSuboptimalAbsoluteDiff()

#### getSuboptimalPercentDiff

    public float getSuboptimalPercentDiff()

#### getTemperature

    public double getTemperature()

#### getTurboFoldCT

    public String getTurboFoldCT(int index)

#### getTurboFoldSaveFile

    public String getTurboFoldSaveFile(int index)

#### getTurboFoldSequenceSetData

    public String getTurboFoldSequenceSetData()

#### readDynalignAlignmentConstraintsFile

    public String readDynalignAlignmentConstraintsFile(String file)

#### readFoldingConstraintsFile

    public String readFoldingConstraintsFile(String file,
                                    int strand)

#### readSequenceData

    public void readSequenceData(String file)

#### runAllSub

    public String runAllSub(String ct,
                   float percent,
                   double absolute)

#### runBifold

    public String runBifold(String ctFile,
                   float percent,
                   int maxStructures,
                   int windowSize,
                   boolean saveFile,
                   boolean intraForbidden)

#### runBipartition

    public String runBipartition(String pfsFile)

#### runDynalign

    public String runDynalign(String ctFile1,
                     String ctFile2,
                     String saveFile,
                     String alignFile,
                     double percent,
                     int structures,
                     int windowStr,
                     int windowAli,
                     float gap,
                     boolean isInsert)

#### runDynalignRefold

    public String runDynalignRefold(String ctFile1,
                           String ctFile2,
                           String alignFile,
                           int percent,
                           int structures,
                           int windowStr,
                           int windowAli)

#### runEfn2

    public String runEfn2(String outFile,
                 boolean writeDetails)

#### runFold

    public String runFold(String ctFile,
                 int percent,
                 int structures,
                 int window,
                 boolean save)

#### runMaxExpect

    public String runMaxExpect(String ctFile,
                      double score,
                      int structures,
                      int window,
                      double gamma)

#### runMultilign

    public String runMultilign(int percent,
                      int maxStructures,
                      int bpWindow,
                      int alignWindow,
                      double gap,
                      boolean insert,
                      double maxDsvChange,
                      int maxPairs,
                      int cycles,
                      String alignFile,
                      boolean saveFiles,
                      boolean isRNA)

#### runOligoScreen

    public String runOligoScreen(String in,
                        String out,
                        boolean isRNA)

#### runOligoWalk

    public String runOligoWalk(String report,
                      int mode,
                      String chemistry,
                      boolean suboptimal,
                      int length,
                      int amount,
                      String unit,
                      int start,
                      int stop)

#### runPartition

    public String runPartition(String pfsFile)

#### runPseudoknotPrediction

    public String runPseudoknotPrediction(String ctFile,
                                 int iterations,
                                 int helix)

#### runPseudoknotRemoval

    public String runPseudoknotRemoval(String ctFile,
                              boolean minimize)

#### runRefold

    public String runRefold(String ctFile,
                   int percent,
                   int structures,
                   int window)

#### runStochastic

    public String runStochastic(String outFile,
                       int ensemble,
                       int seed)

#### runTurboFoldMaximumExpectedAccuracy

    public String runTurboFoldMaximumExpectedAccuracy(double turboGamma,
                                             int turboIterations,
                                             double percent,
                                             int structures,
                                             int window,
                                             double meaGamma)

#### runTurboFoldPseudoknot

    public String runTurboFoldPseudoknot(double turboGamma,
                                int turboIterations,
                                int pkIterations,
                                int helix)

#### runTurboFoldThreshold

    public String runTurboFoldThreshold(double turboGamma,
                               int turboIterations,
                               double threshold)

#### setCleavedNucleotide

    public String setCleavedNucleotide(int nuc,
                              int strand)

#### setDoubleStrandedNucleotide

    public String setDoubleStrandedNucleotide(int nuc,
                                     int strand)

#### setDynalignAlignmentConstraint

    public String setDynalignAlignmentConstraint(int nuc1,
                                        int nuc2)

#### setForcedHelix

    public String setForcedHelix(int nuc1,
                        int nuc2,
                        int length,
                        int strand)

#### setMaxLoop

    public void setMaxLoop(int newLoop)

#### setMaxPair

    public void setMaxPair(int newPair)

#### setModifiedNucleotide

    public String setModifiedNucleotide(int nuc,
                               int strand)

#### setProhibitedHelix

    public String setProhibitedHelix(int nuc1,
                            int nuc2,
                            int length,
                            int strand)

#### setSequenceComment

    public void setSequenceComment(String comment)

#### setSequenceData

    public void setSequenceData(String data)

#### setSequenceTitle

    public void setSequenceTitle(String title)

#### setSHAPEFile

    public void setSHAPEFile(String file)

#### setSHAPEParam1

    public void setSHAPEParam1(double value)

#### setSHAPEParam2

    public void setSHAPEParam2(double value)

#### setSHAPEType

    public void setSHAPEType(boolean isEnergy)

#### setSingleStrandedNucleotide

    public String setSingleStrandedNucleotide(int nuc,
                                     int strand)

#### setTemperature

    public void setTemperature(double newTemp)

#### writeDynalignAlignmentConstraintsFile

    public void writeDynalignAlignmentConstraintsFile(String file)

#### writeFastaFile

    public String writeFastaFile(String file)

#### writeFoldingConstraintsFile

    public String writeFoldingConstraintsFile(String file,
                                     int strand)

#### writeSequenceFile

    public String writeSequenceFile(String file)