# Generated by roxygen2: do not edit by hand

export(alignChromatogramsCpp)
export(alignTargetedRuns)
export(alignToRoot4)
export(areaIntegrator)
export(childXICs)
export(constrainSimCpp)
export(createMZML)
export(createSqMass)
export(doAffineAlignmentCpp)
export(doAlignmentCpp)
export(getAlignObj)
export(getAlignObjs)
export(getAlignedTimes)
export(getAlignedTimesCpp)
export(getAlignedTimesFast)
export(getBaseGapPenaltyCpp)
export(getChildXICpp)
export(getChildXICs)
export(getChromSimMatCpp)
export(getChromatogramIndices)
export(getFeatures)
export(getGlobalAlignMaskCpp)
export(getGlobalAlignment)
export(getMZMLpointers)
export(getMultipeptide)
export(getNativeIDs)
export(getPeptideScores)
export(getPrecursorByID)
export(getPrecursorIndices)
export(getPrecursors)
export(getRTdf)
export(getRefRun)
export(getRunNames)
export(getSeqSimMatCpp)
export(getTransitions)
export(getXICs)
export(getXICs4AlignObj)
export(get_ropenms)
export(imputeChromatogram)
export(mapIdxToTime)
export(mstAlignRuns)
export(mstScript1)
export(mstScript2)
export(otherChildXICpp)
export(paramsDIAlignR)
export(plotAlignedAnalytes)
export(plotAlignmentPath)
export(plotAnalyteXICs)
export(plotXICgroup)
export(progAlignRuns)
export(progComb3)
export(progSplit2)
export(progSplit4)
export(progTree1)
export(recalculateIntensity)
export(reduceXICs)
export(script1)
export(script2)
export(sgolayCpp)
export(smoothXICs)
export(splineFillCpp)
export(updateFileInfo)
exportClasses(AffineAlignObj)
exportClasses(AffineAlignObjLight)
exportClasses(AffineAlignObjMedium)
exportClasses(AlignObj)
exportMethods(as.list)
import(DBI)
import(RMSNumpress)
import(RSQLite)
import(ape)
import(data.table)
import(phangorn)
import(reticulate)
importFrom(Rcpp,sourceCpp)
importFrom(ape,Ntip)
importFrom(bit64,NA_integer64_)
importFrom(data.table,":=")
importFrom(data.table,':=')
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,data.table)
importFrom(data.table,fifelse)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setDT)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(dplyr,"%>%")
importFrom(dplyr,pull)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(pracma,polyfit)
importFrom(rlang,.data)
importFrom(stats,ksmooth)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,loess.control)
importFrom(stats,predict)
importFrom(tidyr,gather)
importFrom(zoo,coredata)
importFrom(zoo,na.approx)
importFrom(zoo,na.locf)
importFrom(zoo,na.spline)
importFrom(zoo,zoo)
useDynLib(DIAlignR, .registration = TRUE)
