Methods
Modifier and Type |
Method and Description |
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) |