useDynLib(TargetSearch)

import("methods")

importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
           "matplot", "par", "plot", "plot.new", "points", "text",
           "title")

importFrom("grDevices", "dev.off", "pdf")

importFrom("stats", "approx", "cor", "cutree", "dist", "hclust", "lm",
           "median", "predict", "sd", "smooth.spline")

importFrom("tcltk", ".Tcl", "tclServiceMode", "tclvalue", "tclvalue<-",
           "tclVar", "tkbutton", "tkcheckbutton", "tkchooseDirectory",
           "tkconfigure", "tkdestroy", "tkentry", "tkfocus", "tkframe",
           "tkgetOpenFile", "tkgetSaveFile", "tkgrid", "tklabel",
           "tkmessageBox", "tkpack", "tkradiobutton", "tktitle<-",
           "tktoplevel", "tkwm.deiconify", "tkwm.iconbitmap",
           "tkProgressBar", "setTkProgressBar")

importFrom("utils", "edit", "head", "installed.packages", "read.delim",
           "setTxtProgressBar", "txtProgressBar", "write.table")

importFrom("ncdf4", "nc_open", "ncvar_get", "nc_close")

exportClasses(
	"tsLib",
	"tsRim",
	"tsSample",
	"tsMSdata",
	"tsProfile"
)

exportMethods(
	"rimMass",
	"rimMass<-",
	"rimLimits",
	"rimLimits<-",
	"rimStandard",
	"rimStandard<-",
	"CDFfiles",
	"CDFfiles<-",
	"RIfiles",
	"RIfiles<-",
	"CDFpath",
	"CDFpath<-",
	"RIpath",
	"RIpath<-",
	"sampleData",
	"sampleData<-",
	"sampleNames",
	"sampleNames<-",
	"sampleDays",
	"sampleDays<-",
	"refLib",
	"libId",
	"medRI",
	"medRI<-",
	"selMass",
	"selMass<-",
	"topMass",
	"topMass<-",
	"quantMass",
	"quantMass<-",
	"spectra",
	"spectra<-",
	"libName",
	"libName<-",
	"libRI",
	"libRI<-",
	"libData",
	"libData<-",
	"RIdev",
	"RIdev<-",
	"retIndex",
	"retIndex<-",
	"retTime",
	"retTime<-",
	"Intensity",
	"Intensity<-",
	"as.list.tsMSdata",
	"as.list.tsProfile",
	"profileInfo",
	"profileInfo<-",
	"profileInt",
	"profileInt<-",
	"profileRI",
	"profileRI<-",
	"profileRT",
	"profileRT<-",
	"fileFormat",
	"fileFormat<-",
	"show"
)

export(
	"FAMEoutliers",
	"FindPeaks",
	"medianRILib",
	"Profile",
	"sampleRI",
	"ImportLibrary",
	"ImportLibrary.tab",
	"ImportLibrary.msp",
	"ImportSamples",
	"ImportSamplesFromDir",
	"ImportFameSettings",
	"NetCDFPeakFinding",
	"peakCDFextraction",
	"peakFind",
	"plotFAME",
	"plotRIdev",
	"plotAllRIdev",
	"plotPeakSimple",
	"plotPeak",
	"plotSpectra",
	"plotAllSpectra",
	"quantMatrix",
	"ProfileCleanUp",
	"RIcorrect",
	"rt2ri",
	"ri2rt",
	"Write.Results",
	"writeMSP",
	"baseline",
	"baselineCorrection",
	"fixRIcorrection",
	"TargetSearchGUI",
	"writeLibText",
	"bin2text",
	"text2bin",
	"riMatrix",
	"fixRI"
)
