NAMESPACE

useDynLib(xcms)

import("methods")
importFrom("graphics", "plot", "image")
importFrom("mzR", "peaks", "close", "openMSfile", "header")

export(
       "etg",
       "medianFilter",
       "retexp",
       "specNoise",
       "specPeaks",
       "SSgauss",
       "msn2xcmsRaw",
       "verify.mzQuantML",
       "xcmsRaw",
       "xcmsSet",
       "xcmsFragments",
       "xcmsPapply"
       )

S3method(plot, xcmsEIC)

S3method(split, xcmsSet)
S3method(c, xcmsSet)

S3method(split, xcmsRaw)

exportClasses(
              "xcmsEIC",
              "xcmsPeaks",
              "xcmsRaw",
              "xcmsSet",
              "xcmsFragments",
              "xcmsSource",
              "xcmsFileSource"
              )

exportMethods(
              "absent",
              "AutoLockMass",
              "calibrate",
              "collect",
              "deepCopy",
              "filepaths",
              "filepaths<-",
              "diffreport",
              "findMZ",
              "findneutral",
              "fillPeaks",
              "fillPeaks.MSW",
              "fillPeaks.chrom",
              "findPeaks.centWave",
              "findPeaks.massifquant",
              "findPeaks.matchedFilter",
              "findPeaks.MSW",
              "findPeaks",
              "getEIC",
              "getPeaks",
              "getScan",
              "getMsnScan",
              "getSpec",
              "group",
              "group.density",
              "group.mzClust",
              "group.nearest",
              "groupidx",
              "groupidx<-",
              "groupnames",
              "groups",
              "groups<-",
              "groupval",
              "image",
              "mzrange",
              "peaks",
              "peaks<-",
              "peakTable",
              "phenoData",
              "phenoData<-",
              "plotChrom",
              "plotEIC",
              "plotPeaks",
              "plotRaw",
              "plotrt",
              "plotScan",
              "plotSpec",
              "plotSurf",
              "plotTIC",
              "plotTree",
              "present",
              "profinfo",
              "profinfo<-",
              "profMedFilt",
              "profMethod",
              "profMethod<-",
              "profMz",
              "profRange",
              "profStep",
              "profStep<-",
              "progressCallback",
              "progressCallback<-",
              "rawEIC",
              "rawMat",
              "retcor",
              "retcor.peakgroups",
              "retcor.obiwarp",
              "revMz",
              "rtrange",
              "sampclass",
              "sampclass<-",
              "sampnames",
              "sampnames<-",
              "specDist",
              "specDist.cosine",
              "specDist.meanMZmatch",
              "specDist.peakCount",
              "show",
              "sortMz",
              "stitch",
              "write.cdf",
              "write.mzdata",
              "write.mzQuantML",
              "xcmsSource",
              "loadRaw"
              )