NAMESPACE

useDynLib(CAMERA)

import("methods")
import(xcms, except=c(plot))

importFrom("RBGL", "highlyConnSG")
importFrom("graph", "ftM2graphNEL")
importFrom("Hmisc", "rcorr")
importMethodsFrom("graph", "addNode", "nodes")
importFrom("graphics", "legend", "plot", "points", "strheight", "text")
importFrom("grDevices", "rgb")
importFrom("stats", "cor.test")
importFrom("utils", "flush.console", "object.size", "read.table")
importFrom("igraph", "graph.data.frame", "label.propagation.community")


importClassesFrom(Biobase, "Versioned")
importFrom(Biobase, validMsg)

export("annotate",
       "annotateDiffreport",
       "cleanParallel",
       "combinexsAnnos",
       "getIsotopeCluster",
       "getpspectra",
       "findKendrickMasses",
       "findNeutralLoss", 
       "findNeutralLossSpecs",
       "pspec2metfrag",
       "pspec2metfusion",
       "xsAnnotate", 
       "compoundQuantiles",
       "compoundLibraries", 
       "massWindowSizes")

exportClasses("xsAnnotate")
exportClasses("compoundQuantiles")
exportMethods("groupFWHM")
exportMethods("findIsotopes", "findIsotopesWithValidation")
exportMethods("getAtomCount", "getIsotopeProportion")
exportMethods("groupCorr")
exportMethods("groupDen")
exportMethods("findAdducts")
exportMethods("show")
exportMethods("plotEICs")
exportMethods("plotPsSpectrum")
exportMethods("getPeaklist")
exportMethods("getReducedPeaklist")
exportMethods("getAllPeakEICs")
exportMethods("calcPC",
	      "calcPC.lpc",
	      "calcPC.hcs")
exportMethods("calcCiS",
	      "calcCaS",
	      "calcIsotopes")

exportClasses("ruleSet")
exportMethods("setDefaultLists",
              "readLists",
              "setDefaultParams",
              "setParams",
              "generateRules")