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R

ReadFile - Class in <Unnamed>
Gives a whole containing of a file in a single String.
runAccAnalysis(int, File, int, int, int, int, int) - Method in class ParamAnalysis
Analyze solvent accessibility coefficient of variation (accVarCoeff) in file.
runExposeAnalysis(int, File, int, int, int, int, int, int, int, List<Integer>, String) - Method in class ParamAnalysis
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal).
runPredictedAccAnalysis(int, List<double[]>, int, int, int, List<Integer>) - Method in class ParamAnalysis
Analyze solvent accessibility coefficient of variation (accVarCoeff) for ACC predicted with ACCpro.
runPredictedAccAnalysis(int, File, int, int, int, List<Integer>, List<Integer>) - Method in class ParamAnalysis
Analyze solvent accessibility coefficient of variation (accVarCoeff) for ACC predicted with ACCpro.
runPredictedExposeAnalysis(int, List<double[]>, int, int, int, List<Integer>) - Method in class ParamAnalysis
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal) on the basis of RSA predicted with ACCpro.
runPredictedExposeAnalysis(int, File, int, int, int, List<Integer>, List<Integer>) - Method in class ParamAnalysis
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal) on the basis of RSA predicted with ACCpro.
runPredictedSsAnalysis(int, List<double[]>, int, int, int, String, List<Character>) - Method in class ParamAnalysis
Analyze occurrence of chosen SS in top results on the basis of SSpro prediction.
runPredictedSsAnalysis(int, File, int, int, int, String, List<Character>, List<Integer>) - Method in class ParamAnalysis
Analyze occurrence of chosen SS in top results on the basis of SSpro prediction.
runRelatAccAnalysis(int, File, int, int, int, int, int, int, int) - Method in class ParamAnalysis
Analyze relative solvent accessibility coefficient of variation (accVarCoeff).
runSeparationAnalysis(int, List<double[]>, int, int, int) - Method in class ParamAnalysis
Analyze separation reduction in a list with data (sepReduction).
runSeparationAnalysis(int, File, int, int, int) - Method in class ParamAnalysis
Analyze separation reduction in a file (sepReduction).
runSpreadAnalysis(int, List<double[]>, int, int, int, int) - Method in class ParamAnalysis
Analyze several statistics of the data column in a list with data (variationCoeff, quartileSpread, standDev, dcaSpread, robVariationCoeff, quartileVarCoeff).
runSpreadAnalysis(int, File, int, int, int, int) - Method in class ParamAnalysis
Analyze several statistics of the data column in a file (variationCoeff, quartileSpread, standDev, dcaSpread, robVariationCoeff, quartileVarCoeff).
runSsAnalysis(int, File, int, int, int, int, int, String, List<Character>) - Method in class ParamAnalysis
Analyze occurrence of chosen SS in top results.
runTpAnalysis(int, File, int, int, int, int, double) - Method in class ParamAnalysis
Analyze TP rate in a set of files (TPrates).
runTpAnalysis(int, File, int, int, int, int) - Method in class ParamAnalysis
Analyze TP rate in a set of files (TPrates).
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