###
### NAMESPACE
###

import(methods)
import(TDA)

importFrom("graphics",
           "abline", "legend", "lines", "points",
           "par", "mtext", "title")
importFrom("stats",
           "dexp", "lm", "optimize", "predict", "runif", "sd",
           "dgamma", "optim","density", "loess", "ecdf", "p.adjust",
           "approx", "quantile")
importFrom("grDevices",
           "colorRampPalette")
importFrom("Mercator",
           "downsample", "Mercator", "addVisualization")
importFrom("ClassDiscovery",
           "distanceMatrix", "SamplePCA")
importFrom("splines", "bs")
importFrom("circlize",
           "circlize", "colorRamp2",
           "circos.clear", "circos.par", "circos.heatmap")
importFrom("rgl",
           "open3d", "bg3d", "view3d", "axes3d",
           "spheres3d", "lines3d", "title3d")
importFrom("ClassComparison", "MultiWilcoxonTest",
           "probDiff")
importMethodsFrom("ClassComparison", "cutoffSignificant", "hist")

exportMethods("plot", "hist", "lines", "points", "image", "cutoffSignificant")

## Rewrite Rips diagrams using index-offfstes instead of
## hard-wired coordinates
export("disentangle")

## objects for primary plotting routines
exportClasses("Cycle", "Feature", "LoopCircos")
export("Cycle", "Feature", "LoopCircos")

## pick out cycles
export("getCycle", "cycleSupport")

## build circos plot
export("angleMeans")

## cycle significance by empirical Bayes
exportClasses("ExpoFit", "EBexpo")
export("ExpoFit", "EBexpo")
export("tailHisto", "cutoff")

#export("gammaFit")

exportClasses("Projection")
export("Projection")
export("voidPlot", "voidFeature")

exportClasses("LoopFeature")
export("LoopFeature")

export("LDPC", "takens")

