import(graphics)
import(Biobase)

importFrom(plyr,llply)
## not needed really, using unexported xcms:::ramp* only
importFrom(xcms,xcmsRaw) 

importFrom(IRanges,IRanges,sapply)
importClassesFrom(IRanges,IRanges)

export(readMzXMLData,
       formatRt,
       extractSpectra,
       extractPrecSpectra)

exportClasses(pSet,
              MIAPE,
              MSnExp,
              MSnProcess,
              MSnSet,
              Spectrum, Spectrum1, Spectrum2,
              ReporterIons)

exportMethods(show,"[","[[",
              fileNames,
              qual,
              length,
              plot,
              plot2d,
              spectra,
              processingData,
              peaksCount,
              clean,
              removePeaks,
              intensity,
              mz,
              tic,
              fromFile,
              precursorMz,
              precursorIntensity,
              precursorCharge,
              acquisitionNum,
              rtime,
              peaksCount,
              msLevel,
              collisionEnergy,
              polarity,
              trimMz,
              quantify,
              header,
              dim,
              multiplex,
              multiLabels,
              width,
              reporterNames,"reporterNames<-",
              reporterColours,reporterColors)
## methods NOT exported
## curveStats
## ms1scan
## "precursorCharge<-"
## ratios
## normalise

