useDynLib("prada")

importClassesFrom(Biobase, AnnotatedDataFrame)
importClassesFrom(methods, ANY, character, data.frame, environment,
                  "function", integer, list, logical, matrix, missing,
                  numeric)
importMethodsFrom(Biobase, description, "description<-", exprs,
                  "exprs<-", pData, "pData<-", phenoData,
                  "phenoData<-", sampleNames, varLabels, varMetadata)
importMethodsFrom(methods, show)
importFrom(BiocGenerics, colnames, nrow, ncol)
importFrom(Biobase, listLen, multiassign, read.AnnotatedDataFrame)
importFrom(graphics, barplot, locator, par, plot.new, points,
           polygon, segments, smoothScatter, title)
importFrom(grDevices, colorRampPalette, densCols, dev.cur, dev.off)
importFrom(grid, convertHeight, convertWidth, convertX, convertY,
           current.transform, current.viewport, current.vpTree, gpar,
           grid.circle, grid.lines, grid.polygon, grid.rect, grid.text,
           grid.yaxis, popViewport, pushViewport, unit, viewport)
importFrom(MASS, cov.rob)
importFrom(methods, "@<-", is, new, validObject)
importFrom(RColorBrewer, brewer.pal)
importFrom(rrcov, CovMcd)
importFrom(stats4, plot)
importFrom(utils, assignInNamespace, getFromNamespace, read.table,
           select.list)


export("analysePlate", "as.all",
       "barploterrbar", "combineFrames",
       "csApply", "fitNorm2", "getPradaPar",
       "plotNorm2", "devDims",
       "plotPlate", "readCytoSet",
       "readFCS", "read.fcs",
       "removeCensored", "setPradaPars",
       "thresholds", "threePanelPlot",
       "devRes", ".drawCircle", ".drawPie",
       "vpLocation", "touchFCS", "combineGates",
       "progress", "updateProgress", "killProgress")


S3method("$", "cytoFrame")
S3method("range", "cytoFrame")
exportClasses("cytoFrame", "cytoSet", "gate", "gateSet")
exportMethods("colnames", "colnames<-",
              "description", "description<-",
              "exprs", "exprs<-",
              "length", "[", "[[", "[[<-",
              "pData", "phenoData", "phenoData<-",
              "show", "plot", "gate", "applyGate",
              "drawGate", "gate<-", "names", "names<-",
              "as.gateSet", "nrow", "ncol", "appendGates", "lines",
              "split")
