##
## NAMESPACE file for the xps package.
##
useDynLib(xps)

## packages
import(graphics, methods)

## S4 classes
exportClasses(ProjectInfo,
              TreeSet,
              Filter,
              PreFilter,
              UniFilter,
              SchemeTreeSet,
              ProcesSet,
              DataTreeSet,
              ExprTreeSet,
              CallTreeSet,
              FilterTreeSet,
              AnalysisTreeSet)

## class ProjectInfo
exportMethods("arrayInfo",
              "arrayInfo<-",
              "authorInfo",
              "authorInfo<-",
              "biopsyInfo",
              "biopsyInfo<-",
              "cellineInfo",
              "cellineInfo<-",
              "datasetInfo",
              "datasetInfo<-",
              "hybridizInfo",
              "hybridizInfo<-",
              "primcellInfo",
              "primcellInfo<-",
              "projectInfo",
              "projectInfo<-",
              "sampleInfo",
              "sampleInfo<-",
              "show",
              "sourceInfo",
              "sourceInfo<-",
              "tissueInfo",
              "tissueInfo<-",
              "treatmentInfo",
              "treatmentInfo<-")

## class TreeSet
exportMethods("export",
              "fileDir",
              "fileDir<-",
              "initialize",
              "root.browser",
              "rootFile",
              "rootFile<-",
              "setName",
              "setName<-",
              "setType",
              "setType<-",
              "treeNames")

## class SchemeTreeSet
exportMethods("attachMask",
              "chipMask",
              "chipMask<-",
              "chipName",
              "chipType",
              "chipType<-",
              "ncols",
              "nrows",
              "probeInfo",
              "removeMask")

## class ProcesSet
exportMethods("boxplot",
              "getTreeData",
              "hist",
              "mboxplot",
              "schemeFile",
              "schemeFile<-",
              "schemeSet",
              "schemeSet<-",
              "validData")

## class DataTreeSet
exportMethods("addData",
              "attachBgrd",
              "attachInten",
              "background",
              "background<-",
              "bgtreeNames",
              "image",
              "intensity",
              "intensity<-",
              "mm",
              "pm",
              "pmplot",
              "rawCELName",
              "removeBgrd",
              "removeInten",
              "validBgrd",
              "xpsBgCorrect",
              "xpsDABGCall",
              "xpsMAS5Call",
              "xpsMAS5",
              "xpsMAS4",
              "xpsNormalize",
              "xpsPreprocess",
              "xpsSummarize",
              "xpsRMA")

## class ExprTreeSet
exportMethods("exprs",
              "exprs<-",
              "exprType",
              "exprType<-",
              "mvaplot",
              "normType",
              "normType<-",
              "se.exprs",
              "xpsPreFilter",
              "xpsUniFilter")

## class CallTreeSet
exportMethods("pvalData",
              "pvalData<-",
              "presCall",
              "presCall<-",
              "validCall",
              "callplot")

## class Filter
exportMethods("numberFilters")

## class PreFilter
exportMethods("callFilter",
              "callFilter<-",
              "cvFilter",
              "cvFilter<-",
              "diffFilter",
              "diffFilter<-",
              "gapFilter",
              "gapFilter<-",
              "highFilter",
              "highFilter<-",
              "lowFilter",
              "lowFilter<-",
              "madFilter",
              "madFilter<-",
              "quantileFilter",
              "quantileFilter<-",
              "ratioFilter",
              "ratioFilter<-",
              "varFilter",
              "varFilter<-")

## class UniFilter
exportMethods("fcFilter",
              "fcFilter<-",
              "unitestFilter",
              "unitestFilter<-",
              "uniTest",
              "uniTest<-")

## class FilterTreeSet
exportMethods("callTreeset",
              "exprTreeset")

## class AnalysisTreeSet
exportMethods("filterTreeset",
              "validFilter",
              "volcanoplot")

## functions
export(import.expr.scheme, import.exon.scheme, import.genome.scheme, import.data)
export(export.scheme, export.data, export.expr, export.call, export.filter, export.root)
export(rma, mas4, mas5, mas5.call, dabg.call)
export(bgcorrect, normalize, summarize, express)
export(bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc)
export(normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu)
export(summarize.mas4, summarize.mas5, summarize.rma)
export(boxplot.dev, image.dev, mvaplot.dev)
export(prefilter, unifilter)

## contructor functions
export(ProjectInfo)
export(PreFilter, UniFilter)

## root.functions
export(root.scheme, root.data)
export(root.image)
export(root.graph1D, root.graph2D, root.mvaplot)
export(root.hist1D, root.hist2D, root.hist3D)
export(root.density)

## utility functions
export(xpsOptions, debug.xps)
export(getDatatype, validTreetype)
export(getChipName, getChipType, getNameType, getProbeInfo)
export(getNumberTrees, getTreeNames)
export(isROOTFile, existsROOTFile)
export(type2Exten)


