useDynLib(pegas, .registration = TRUE)

export(amova, as.igraph.haploNet, as.loci, as.network.haploNet,
       diffHaplo, dist.haplotype.loci, expand.genotype, Fst, genind2loci,
       geod, geoTrans, getAlleles, getGenotypes, getPloidy, H, haploNet,
       haploFreq, haplotype, heterozygosity, hw.test, is.phased, is.snp,
       LD, LD2, loci2genind, mst, MMD, nuc.div, proba.genotype, R2.test,
       read.gtx, read.loci, read.vcf, replot, rr.test, site.spectrum,
       tajima.test, theta.h, theta.k, theta.msat, theta.s, theta.tree,
       write.loci)

## we try to limit the imports for the moment (2013-08-12)
importFrom(ape, BOTHlabels, branching.times, base.freq, dist.dna,
           floating.pie.asp, perm.rowscols, rcoal, seg.sites)
importFrom(adegenet, df2genind, genind2df)
importFrom(graphics, plot)
## importFrom(stats, density)
importFrom(utils, edit)

S3method(print, amova)

S3method(as.loci, character)
S3method(as.loci, data.frame)
S3method(as.loci,factor)
S3method(as.loci, genind)

S3method(haplotype, DNAbin)
S3method(haplotype, loci)

#S3method(as.igraph, haploNet)
#S3method(as.network, haploNet)
S3method(plot, haploNet)

S3method("[", haplotype)
S3method(plot, haplotype)
S3method(print, haplotype)
S3method(sort, haplotype)

S3method(plot, haplotype.loci)

S3method("[", loci)
S3method(cbind, loci)
S3method(edit, loci)
S3method(print, loci)
S3method(rbind, loci)
S3method(summary, loci)

S3method(plot, spectrum)

S3method(plot, summary.loci)
S3method(print, summary.loci)
