useDynLib(GeneR)

##exportPattern("^[^\\.]")

export(.seqSize,nSeq,.paramFromIndex)

##export("|.segSet","-.segSet","&.segSet","|.globalSeg","-.globalSeg","&.globalSeg")

export(as.segSet,or.segSet,Xor.segSet,not.segSet,and.segSet,plot.segSet,
	as.data.frame.segSet,as.matrix.segSet,"as.globalSeg","or.globalSeg",
	"Xor.globalSeg","not.globalSeg","and.globalSeg","size.globalSeg",
	"Length.globalSeg","Max.globalSeg","Min.globalSeg","as.matrix.globalSeg",
	"plot.globalSeg","range.globalSeg",plot.profile,and.default,or.default,
	Xor.default,not.default,size.default,Min.default,Max.default,Length.default)


export(insertSeq,strComp,strCompoSeq,placeString,revComp,getSeq,exactWord,
	dnaToRna,rnaToDna,assemble,concat,compoSeq,appendSeq,
	bankDensityProfile,densityProfile,
	freeSeq,freeAllSeq,sizeSeq,sliceSegment,seqSkew,GCcontent,setStrand,
	getStrand,setBegSeq,getBegSeq,setSeqSize,getSeqSize,getEndSeq,setAccn,
	getAccn,setParam,getParam,RtoA,AtoT,TtoA,RtoT,TtoR,AtoR,indexFasta,indexGbk,
	indexEmbl,makeIndex,deleteCR,posMaskedSeqFile,posMaskedSeq,upperSeq,
	lowerSeq,getOrfs,maxOrf,strTranslate,translate,showTable,readEmblLocation,
	readGbkLocation,readSeq,sizeSeqEmbl,sizeSeqGbk,sizeSeqFasta,fastaDescription,
	readFasta,readGbk,readEmbl,randomSeq,shuffleSeq,
	strReadEmbl,strReadGbk,strReadFasta,or,Xor,and,not,size,Min,Max,
	Length,.minimalSeg,relist,relistage,xorRecouvr,seqSrs,seqNcbi,writeEmblLine,
	writeEmblComment,writeEmblSeq,writeFasta,strWriteFasta,mask,unionSeg,
	bankSummary)

export (readEmblDescript,.transf.limites)

export(Match)

#importFrom(methods,as)

S3method(Xor,default)
S3method(and,default)
S3method(or,default)
S3method(not,default)
S3method(size,default)
S3method(Min,default)
S3method(Max,default)
S3method(Length,default)

#S3method(as,segSet)
S3method(or,segSet)
S3method("|",segSet)
S3method(Xor,segSet)
S3method(not,segSet)
S3method("-",segSet)
S3method(and,segSet)
S3method("&",segSet)
S3method(plot,segSet)
S3method(as.data.frame,segSet)
# S3method(as,globalSeg)
S3method(or,globalSeg)
S3method("|",globalSeg)
S3method(Xor,globalSeg)
S3method(not,globalSeg)
S3method("-",globalSeg)
S3method(and,globalSeg)
S3method("&",globalSeg)
S3method(size,globalSeg)
S3method(Length,globalSeg)
S3method(Max,globalSeg)
S3method(Min,globalSeg)
S3method(as.matrix,globalSeg)
S3method(plot,globalSeg)
S3method(range,globalSeg)
S3method(plot,profile)

