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C

calculateColtPCA(DoubleMatrixDataset<String, String>, DoubleMatrix2D, String, Integer) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

Calculate Colt PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.

calculateMtjPCA(DoubleMatrixDataset<String, String>, DoubleMatrix2D, String, Integer) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

Calculate MTJ PCA scores Matrix contains the correlation, covariation, bray curtis distance or city block distance.

D

DEFAULT_NUMBER_FORMATTER - Static variable in class nl.umcg.bondermj.pcoa.DoPcoa

DoPcoa - Class in nl.umcg.bondermj.pcoa

DoPcoa() - Constructor for class nl.umcg.bondermj.pcoa.DoPcoa

G

generatePcCorrectedData(String, String, String, int, int, int) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

generatePcCorrectedDataWithSkipping(String, String, String, int, int, int, ArrayList<String>) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

getFileIn() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getLOGGER() - Static method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getMatrixType() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getNumberComponentsToCalc() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getOPTIONS() - Static method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getPackageToUse() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

getThreads() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

I

isCenter() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

isInteger(String) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

isMultiThreading() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

isOverRows() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

isScale() - Method in class nl.umcg.bondermj.pcoa.PcoaParamaters

M

main(String...) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

N

nl.umcg.bondermj.pcoa - package nl.umcg.bondermj.pcoa

P

PcoaParamaters - Class in nl.umcg.bondermj.pcoa

PcoaParamaters(String...) - Constructor for class nl.umcg.bondermj.pcoa.PcoaParamaters

PcoaParamaters.MatrixType - Enum in nl.umcg.bondermj.pcoa

PcoaParamaters.PackageToUse - Enum in nl.umcg.bondermj.pcoa

printHelp() - Static method in class nl.umcg.bondermj.pcoa.PcoaParamaters

R

regressOutPCs(DoubleMatrixDataset<String, String>, String, String, String, int, int) - Static method in class nl.umcg.bondermj.pcoa.DoPcoa

V

valueOf(String) - Static method in enum nl.umcg.bondermj.pcoa.PcoaParamaters.MatrixType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum nl.umcg.bondermj.pcoa.PcoaParamaters.PackageToUse

Returns the enum constant of this type with the specified name.

values() - Static method in enum nl.umcg.bondermj.pcoa.PcoaParamaters.MatrixType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum nl.umcg.bondermj.pcoa.PcoaParamaters.PackageToUse

Returns an array containing the constants of this enum type, in the order they are declared.

C D G I M N P R V