useDynLib("oligo")

## Needed from splines
importFrom(splines, ns)

## Needed from affxparser
importFrom(affxparser, createCel, readCel, readCelHeader,
           readCelIntensities, updateCel)

## Needed from graphics
importFrom(graphics, boxplot, hist, image, lines, matplot, par, plot)
importFrom(grDevices, gray)

## Needed from utils
importFrom(utils, packageDescription, read.delim, read.table,
           setTxtProgressBar, txtProgressBar, write.table)

## Needed from methods
importClassesFrom(methods, array, matrix)
importFrom(methods, "@<-", is, new)

## Needed from stats
importFrom(stats, coef, cov, density, dnorm, fitted, kmeans, lm,
           lowess, mad, median, pchisq, quantile, residuals)

## Needed from DBI
importMethodsFrom(DBI, dbGetQuery)

## Needed from Biobase
importClassesFrom(Biobase, ExpressionSet)
importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
                  "annotation<-", experimentData, exprs, featureData,
                  "featureData<-", featureNames, "featureNames<-",
                  "notes<-", pData, phenoData, "phenoData<-", preproc,
                  "preproc<-", rowMedians, sampleNames,
                  "sampleNames<-", varMetadata, combine)
importFrom(Biobase, assayDataElement, assayDataElementReplace)

## Needed from affyio
import(affyio)

## Get everything from oligoClasses
import(oligoClasses)

## Exporting
exportMethods("boxplot",
              "bg",
              "bg<-",
              "db",
              "exprs",
              "getContainer",
              "getX",
              "getY",
              "hist",
              "image",
              "initialize",
              "length",
              "MAplot",
              "mm",
              "mm<-",
              "pm",
              "pm<-",
              "rma")

## Exported functions
export("basecontent",
       "cleanPlatformName",
       "read.celfiles",
       "read.xysfiles",
       "sequenceDesignMatrix",
       "list.celfiles",
       "list.xysfiles",
       "readSummaries",
       "getCrlmmSummaries",
       "getNgsColorsInfo",
       "read.xysfiles2",
       "read.celfiles2",
       "basicRMA")

## Exported functions for CRLMM
export("crlmm",
       "snprma",
       "justSNPRMA",
       "justCRLMM")
