ur_rna.RNAstructureUI

Class RNAstructureBackendCalculator

java.lang.Object

ur_rna.RNAstructureUI.RNAstructureBackendCalculator

public class RNAstructureBackendCalculator
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	swigCMemOwn
private long	swigCPtr

Constructor Summary

Constructors

Modifier	Constructor and Description
	RNAstructureBackendCalculator()
protected	RNAstructureBackendCalculator(long cPtr, boolean cMemoryOwn)

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

swigCMemOwn

protected transient boolean swigCMemOwn

swigCPtr

private transient 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(java.lang.String seqFile,
                              java.lang.String ctFile)

addTurboFoldTuple

public void addTurboFoldTuple(java.lang.String seqFile,
                              java.lang.String ctFile)

addTurboFoldTuple

public void addTurboFoldTuple(java.lang.String seqFile,
                              java.lang.String ctFile,
                              java.lang.String pfsFile)

buildAccessFoldDataStructure

public java.lang.String buildAccessFoldDataStructure(java.lang.String file1,
                                                     java.lang.String file2,
                                                     boolean isRNA)

buildAllSubDataStructure

public java.lang.String buildAllSubDataStructure(java.lang.String file,
                                                 boolean isRNA)

buildBifoldDataStructure

public java.lang.String buildBifoldDataStructure(java.lang.String file1,
                                                 java.lang.String file2,
                                                 boolean isRNA)

buildBipartitionDataStructure

public java.lang.String buildBipartitionDataStructure(java.lang.String file1,
                                                      java.lang.String file2,
                                                      boolean isRNA)

buildDuplexFoldDataStructure

public java.lang.String buildDuplexFoldDataStructure(java.lang.String file1,
                                                     java.lang.String file2,
                                                     boolean isRNA)

buildDynalignDataStructure

public java.lang.String buildDynalignDataStructure(java.lang.String file1,
                                                   java.lang.String file2,
                                                   boolean isRNA)

buildEfn2DataStructure

public java.lang.String buildEfn2DataStructure(java.lang.String file,
                                               boolean isRNA)

buildFoldDataStructure

public java.lang.String buildFoldDataStructure(java.lang.String file,
                                               boolean isRNA)

buildMaxExpectDataStructure

public java.lang.String buildMaxExpectDataStructure(java.lang.String file)

buildOligoScreenDataStructure

public java.lang.String buildOligoScreenDataStructure()

buildOligoWalkDataStructure

public java.lang.String buildOligoWalkDataStructure(java.lang.String file,
                                                    boolean isRNA)

buildPartitionDataStructure

public java.lang.String buildPartitionDataStructure(java.lang.String file,
                                                    boolean isRNA)

buildProbKnotDataStructure

public java.lang.String buildProbKnotDataStructure(java.lang.String file)

buildRefoldDynalignDataStructure

public java.lang.String buildRefoldDynalignDataStructure(java.lang.String file)

buildRefoldSingleDataStructure

public java.lang.String buildRefoldSingleDataStructure(java.lang.String file)

buildRemovePseudoknotsDataStructure

public java.lang.String buildRemovePseudoknotsDataStructure(java.lang.String file,
                                                            boolean isRNA)

buildStochasticDataStructure

public java.lang.String buildStochasticDataStructure(java.lang.String file)

cancelOperation

public void cancelOperation()

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 java.lang.Object

foldOligo

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

getAllOligoData

public java.lang.String getAllOligoData(int height)

getCPtr

protected static long getCPtr(RNAstructureBackendCalculator obj)

getDisplayedOligo

public java.lang.String getDisplayedOligo(int index)

getDynalignAlignmentConstraints

public java.lang.String getDynalignAlignmentConstraints()

getDynalignAlignmentWindowSize

public int getDynalignAlignmentWindowSize()

getDynalignStructureWindowSize

public int getDynalignStructureWindowSize()

getEnvVar

public static java.lang.String getEnvVar(java.lang.String varname)

GetErrorCode

public int GetErrorCode()

getFoldingConstraints

public java.lang.String getFoldingConstraints(int strand)

getFoldWindowSize

public int getFoldWindowSize()

GetFullErrorMessage

public java.lang.String GetFullErrorMessage()

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 java.lang.String getMultilignCT(int index)

getMultilignMaxPairs

public int getMultilignMaxPairs()

getMultilignSequenceSetData

public java.lang.String getMultilignSequenceSetData()

getNumMultilignSequences

public int getNumMultilignSequences()

getNumTurboFoldSequences

public int getNumTurboFoldSequences()

getOligoLabelData

public java.lang.String getOligoLabelData(int index)

getOligoTargetLength

public int getOligoTargetLength()

getOligoTargetSequence

public java.lang.String getOligoTargetSequence()

getProgressNumber

public int getProgressNumber()

getRefoldWindowSize

public int getRefoldWindowSize()

getSaveFile

public java.lang.String getSaveFile()

getSequenceComment

public java.lang.String getSequenceComment()

getSequenceData

public java.lang.String getSequenceData()

getSequenceTitle

public java.lang.String getSequenceTitle()

getStructureType

public java.lang.String getStructureType()

getSuboptimalAbsoluteDiff

public double getSuboptimalAbsoluteDiff()

getSuboptimalPercentDiff

public float getSuboptimalPercentDiff()

getTemperature

public double getTemperature()

getTurboFoldCT

public java.lang.String getTurboFoldCT(int index)

getTurboFoldSaveFile

public java.lang.String getTurboFoldSaveFile(int index)

getTurboFoldSequenceSetData

public java.lang.String getTurboFoldSequenceSetData()

getVersion

public static java.lang.String getVersion()

loadDoubleRNA

public java.lang.String loadDoubleRNA(java.lang.String file1,
                                      java.lang.String file2,
                                      boolean isRNA)

loadDoubleRNA

public java.lang.String loadDoubleRNA(java.lang.String file1,
                                      java.lang.String file2,
                                      boolean isRNA,
                                      int fileType)

loadSingleRNA

public java.lang.String loadSingleRNA(java.lang.String file1,
                                      boolean isRNA)

loadSingleRNA

public java.lang.String loadSingleRNA(java.lang.String file1,
                                      boolean isRNA,
                                      int fileType)

readDynalignAlignmentConstraintsFile

public java.lang.String readDynalignAlignmentConstraintsFile(java.lang.String file)

readFoldingConstraintsFile

public java.lang.String readFoldingConstraintsFile(java.lang.String file,
                                                   int strand)

readSequenceData

public void readSequenceData(java.lang.String file)

runAccessFold

public java.lang.String runAccessFold(java.lang.String ctFile,
                                      float percent,
                                      int maxStructures,
                                      double gamma,
                                      int windowSize,
                                      boolean saveFile)

runAllSub

public java.lang.String runAllSub(java.lang.String ct,
                                  float percent,
                                  double absolute)

runBifold

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

runBipartition

public java.lang.String runBipartition(java.lang.String pfsFile)

runDuplexFold

public java.lang.String runDuplexFold(java.lang.String ctFile,
                                      float percent,
                                      int maxStructures,
                                      int windowSize,
                                      boolean saveFile)

runDynalign

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

runDynalignRefold

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

runEfn2

public java.lang.String runEfn2(java.lang.String outFile,
                                boolean writeDetails)

runFold

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

runMaxExpect

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

runMultilign

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

runOligoScreen

public java.lang.String runOligoScreen(java.lang.String in,
                                       java.lang.String out,
                                       boolean isRNA)

runOligoWalk

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

runPartition

public java.lang.String runPartition(java.lang.String pfsFile)

runPseudoknotPrediction

public java.lang.String runPseudoknotPrediction(java.lang.String ctFile,
                                                int iterations,
                                                int helix)

runPseudoknotRemoval

public java.lang.String runPseudoknotRemoval(java.lang.String ctFile,
                                             boolean minimize)

runRefold

public java.lang.String runRefold(java.lang.String ctFile,
                                  int percent,
                                  int structures,
                                  int window)

runStochastic

public java.lang.String runStochastic(java.lang.String outFile,
                                      int ensemble,
                                      int seed)

runTurboFoldMaximumExpectedAccuracy

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

runTurboFoldMaximumExpectedAccuracy

public java.lang.String runTurboFoldMaximumExpectedAccuracy(double turboGamma,
                                                            int turboIterations,
                                                            double percent,
                                                            int structures,
                                                            int window,
                                                            double meaGamma,
                                                            java.lang.String outAlnFile)

runTurboFoldPseudoknot

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

runTurboFoldPseudoknot

public java.lang.String runTurboFoldPseudoknot(double turboGamma,
                                               int turboIterations,
                                               int pkIterations,
                                               int helix,
                                               java.lang.String outAlnFile)

runTurboFoldThreshold

public java.lang.String runTurboFoldThreshold(double turboGamma,
                                              int turboIterations,
                                              double threshold)

runTurboFoldThreshold

public java.lang.String runTurboFoldThreshold(double turboGamma,
                                              int turboIterations,
                                              double threshold,
                                              java.lang.String outAlnFile)

setCleavedNucleotide

public java.lang.String setCleavedNucleotide(int nuc,
                                             int strand)

setDoubleStrandedNucleotide

public java.lang.String setDoubleStrandedNucleotide(int nuc,
                                                    int strand)

setDynalignAlignmentConstraint

public java.lang.String setDynalignAlignmentConstraint(int nuc1,
                                                       int nuc2)

setEnvVar

public static int setEnvVar(java.lang.String envstr)

setForcedHelix

public java.lang.String setForcedHelix(int nuc1,
                                       int nuc2,
                                       int length,
                                       int strand)

setMaxLoop

public void setMaxLoop(int newLoop)

setMaxPair

public void setMaxPair(int newPair)

setModifiedNucleotide

public java.lang.String setModifiedNucleotide(int nuc,
                                              int strand)

setProhibitedHelix

public java.lang.String setProhibitedHelix(int nuc1,
                                           int nuc2,
                                           int length,
                                           int strand)

setSaveFile

public void setSaveFile(java.lang.String path)

setSequenceComment

public void setSequenceComment(java.lang.String comment)

setSequenceData

public void setSequenceData(java.lang.String data)

setSequenceTitle

public void setSequenceTitle(java.lang.String title)

setSHAPEFile

public void setSHAPEFile(java.lang.String file)

setSHAPEParam1

public void setSHAPEParam1(double value)

setSHAPEParam2

public void setSHAPEParam2(double value)

setSHAPEType

public void setSHAPEType(boolean isEnergy)

setSingleStrandedNucleotide

public java.lang.String setSingleStrandedNucleotide(int nuc,
                                                    int strand)

setTemperature

public void setTemperature(double newTemp)

wasCanceled

public boolean wasCanceled()

writeDynalignAlignmentConstraintsFile

public void writeDynalignAlignmentConstraintsFile(java.lang.String file)

writeFastaFile

public java.lang.String writeFastaFile(java.lang.String file)

writeFoldingConstraintsFile

public java.lang.String writeFoldingConstraintsFile(java.lang.String file,
                                                    int strand)

writeSequenceFile

public java.lang.String writeSequenceFile(java.lang.String file)