importFrom(stats, as.dendrogram)
importFrom(stats, as.hclust)
importFrom(stats, median)
importFrom(stats, quantile)
import(methods)

# The igraph interface

export(add.vertices, delete.edges,
       delete.vertices, ecount, neighbors, incident, get.edges, get.edge.ids)

export("[.igraph", "[[.igraph", "[<-.igraph")

S3method("[", "igraph")
S3method("[[", "igraph")
S3method("[<-", "igraph")

export(edge, edges, vertex, vertices, path,
       "+.igraph", "-.igraph")

S3method("+", "igraph")
S3method("-", "igraph")

# Attributes

export(get.graph.attribute, set.graph.attribute, graph.attributes,
       get.vertex.attribute, set.vertex.attribute, vertex.attributes,
       get.edge.attribute, set.edge.attribute, edge.attributes,
       list.graph.attributes, list.vertex.attributes,
       list.edge.attributes, remove.graph.attribute,
       remove.vertex.attribute, remove.edge.attribute,
       "graph.attributes<-", "vertex.attributes<-", "edge.attributes<-")

# iterators

export(V, E, "$.igraph.vs", "$.igraph.es",
       "[.igraph.vs", "[[.igraph.vs", "[.igraph.es", "[[.igraph.es",
       "[<-.igraph.vs", "[<-.igraph.es", "[[<-.igraph.vs", "[[<-.igraph.es",
       "$<-.igraph.vs", "$<-.igraph.es", "V<-", "E<-",
       print.igraph.vs, print.igraph.es, "%--%", "%->%", "%<-%")

S3method("$", igraph)
S3method("$<-", igraph)
S3method("$", igraph.vs)
S3method("[", igraph.vs)
S3method("[[", igraph.vs)
S3method("[<-", igraph.vs)
S3method("[[<-", igraph.vs)
S3method("$<-", igraph.vs)
S3method("$", igraph.es)
S3method("[", igraph.es)
S3method("[[", igraph.es)
S3method("[<-", igraph.es)
S3method("[[<-", igraph.es)
S3method("$<-", igraph.es)
S3method(print, igraph.vs)
S3method(print, igraph.es)
  
# basic functions, printing

export(is.igraph, is.named, is.weighted, is.bipartite,
       are.connected, print.igraph, str.igraph, summary.igraph,
       is.directed, get.edge)

S3method("str", "igraph")

# structure generators

export(graph, graph.adjacency, graph.star, graph.tree, graph.lattice,
       graph.ring, graph.full, graph.atlas, graph.data.frame, graph.edgelist,
       graph.extended.chordal.ring, line.graph, graph.de.bruijn, graph.kautz,
       graph.formula, graph.famous)

# games

export(erdos.renyi.game, random.graph.game, degree.sequence.game,
       aging.prefatt.game, aging.barabasi.game, aging.ba.game,
       growing.random.game, barabasi.game, ba.game,
       callaway.traits.game, establishment.game, grg.game,
       preference.game, asymmetric.preference.game, connect.neighborhood,
       rewire.edges, watts.strogatz.game, lastcit.game, cited.type.game,
       citing.cited.type.game, bipartite.random.game)

# community structure

export(edge.betweenness.community,
       spinglass.community, walktrap.community,
       edge.betweenness.community.merges, fastgreedy.community,
       community.to.membership)

export(membership, modularity, sizes, algorithm, is.hierarchical, merges,
       cutat, communities, crossing, plot.communities, compare,
       compare.communities, showtrace, code.length, asPhylo, dendPlot,
       create.communities)

S3method("print", communities)
S3method("modularity", communities)
S3method("length", communities)
S3method("as.dendrogram", communities)
S3method("as.hclust", communities)
S3method("asPhylo", communities)
S3method("modularity", igraph)
S3method("dendPlot", communities)
S3method("compare", communities)
S3method("compare", numeric)
S3method("compare", default)

# conversion

export(get.adjacency, get.edgelist, as.directed, as.undirected,
       get.adjlist, get.adjedgelist, igraph.from.graphNEL, 
       igraph.to.graphNEL, get.data.frame)

# fitting, other

export(power.law.fit, running.mean, igraph.sample, srand)

# foreign formats

export(read.graph, write.graph, graph.graphdb)

# layouts

export(layout.auto, layout.random, layout.circle,
       layout.spring, layout.kamada.kawai, layout.lgl,
       layout.fruchterman.reingold.grid, layout.sphere, layout.merge,
       layout.reingold.tilford, layout.norm, piecewise.layout)
export(igraph.drl.default, igraph.drl.coarsen, igraph.drl.coarsest,
       igraph.drl.refine, igraph.drl.final)

# structural properties

export(subgraph, degree, degree.distribution, diameter,
       subcomponent, betweenness, bibcoupling, cocitation,
       shortest.paths, minimum.spanning.tree,
       get.shortest.paths, average.path.length, transitivity,
       get.all.shortest.paths, get.diameter, farthest.nodes,
       constraint, page.rank, reciprocity, rewire,
       graph.density, neighborhood.size, neighborhood, graph.neighborhood,
       graph.coreness, topological.sort, girth, is.loop, is.multiple,
       count.multiple)

# plotting

export(plot.igraph, tkplot, tkplot.close, tkplot.off, tkplot.fit.to.screen,
       tkplot.reshape, tkplot.export.postscript, tkplot.getcoords,
       tkplot.center, tkplot.rotate, tkplot.canvas, tkplot.setcoords,
       rglplot.igraph, rglplot,
       autocurve.edges, vertex.shapes, add.vertex.shape,
       igraph.shape.noclip, igraph.shape.noplot)

S3method(rglplot, igraph)

# components

export(cluster.distribution, is.connected, decompose.graph,
       no.clusters)

# centrality

export(evcent, bonpow, alpha.centrality, subgraph.centrality)
export(igraph.arpack.default, igraph.eigen.default)

# dynamics measurement

export(revolver.d, revolver.error.d,
       revolver.ad, revolver.error.ad,
       revolver.ade, revolver.error.ade,
       revolver.e, revolver.error.e,
       revolver.de, revolver.error.de,
       revolver.l, revolver.error.l,
       revolver.dl, revolver.error.dl,
       revolver.el, revolver.error.el,
       revolver.r, revolver.error.r,
       revolver.ar, revolver.error.ar,
       revolver.di, revolver.error.di,
       revolver.adi, revolver.error.adi,
       revolver.il, revolver.error.il,
       revolver.ir, revolver.error.ir,
       revolver.air, revolver.error.air)

export (revolver.d.d, revolver.p.p)

export (evolver.d)

# isomorphism, motifs

export(graph.isoclass, graph.isomorphic, graph.motifs,
       graph.motifs.est, graph.isocreate, graph.motifs.no,
       graph.isomorphic.vf2, graph.subisomorphic.vf2,
       graph.count.isomorphisms.vf2, graph.count.subisomorphisms.vf2,
       graph.get.isomorphisms.vf2, graph.get.subisomorphisms.vf2)

# operators

export(graph.disjoint.union, "%du%", graph.intersection, "%s%",
       graph.union, "%u%", graph.difference, "%m%",
       graph.complementer, graph.compose, "%c%")

# parameters, config

export(igraph.par, igraph.options, getIgraphOpt, igraphtest, igraph.version)

# console

export(igraph.console, .igraph.progress, .igraph.status)

# flows, cuts, etc.

export(graph.mincut, vertex.connectivity, edge.connectivity,
       edge.disjoint.paths, vertex.disjoint.paths, graph.adhesion,
       graph.cohesion)

# cliques

export(cliques, largest.cliques, maximal.cliques, clique.number,
       independent.vertex.sets, largest.independent.vertex.sets,
       maximal.independent.vertex.sets, independence.number)

# cohesive blocking, this is what remains from the old implementation

S3method(layout.svd, igraph)
export(layout.svd)

# cohesive blocking, new style 

export(blocks, blockGraphs, cohesion, hierarchy, parent,
       plotHierarchy, exportPajek, maxcohesion)

S3method(print, cohesiveBlocks)
S3method(summary, cohesiveBlocks)
S3method(plot, cohesiveBlocks)
S3method(length, cohesiveBlocks)

# arpack

export(arpack)

# tkigraph, demo

export(tkigraph,igraphdemo)

# HRG

S3method(print, igraphHRG)
S3method(print, igraphHRGConsensus)
S3method("as.dendrogram", igraphHRG)
S3method("as.hclust", igraphHRG)
S3method("asPhylo", igraphHRG)
S3method("dendPlot", igraphHRG)

# SCG

export(scg)
S3method(scg, "igraph")
S3method(scg, "matrix")
S3method(scg, "Matrix")

# nexus

export(nexus.get, nexus.list, nexus.info, nexus.search)
S3method(print, nexusDatasetInfo)
S3method(print, nexusDatasetInfoList)
S3method(summary, nexusDatasetInfoList)
S3method("[", nexusDatasetInfoList)

# Sparse data frame

S3method(as.data.frame, igraphSDF)
S3method("[", igraphSDF)
S3method("[<-", igraphSDF)

# convert to igraph

export(as.igraph)
S3method(as.igraph, "igraphHRG")

# Graphlets

export(graphlets, graphlets.project)

# SIR

export(plot.sir, time_bins)
S3method(plot, sir)
S3method(median, sir)
S3method(quantile, sir)
S3method(time_bins, sir)

######################## REST IS GENERATED BY stimulus
export(graph.empty)
export(add.edges)
export(vcount)
export(graph.full.citation)
export(graph.lcf)
export(graph.adjlist)
export(graph.full.bipartite)
export(forest.fire.game)
export(interconnected.islands.game)
export(static.fitness.game)
export(static.power.law.game)
export(k.regular.game)
export(sbm.game)
export(closeness)
export(closeness.estimate)
export(betweenness.estimate)
export(edge.betweenness)
export(edge.betweenness.estimate)
export(page.rank.old)
export(page.rank)
export(induced.subgraph)
export(subgraph.edges)
export(path.length.hist)
export(simplify)
export(is.dag)
export(is.simple)
export(has.multiple)
export(evcent)
export(hub.score)
export(authority.score)
export(arpack.unpack.complex)
export(unfold.tree)
export(is.mutual)
export(maximum.cardinality.search)
export(is.chordal)
export(graph.knn)
export(graph.strength)
export(centralize.scores)
export(centralization.degree)
export(centralization.degree.tmax)
export(centralization.betweenness)
export(centralization.betweenness.tmax)
export(centralization.closeness)
export(centralization.closeness.tmax)
export(centralization.evcent)
export(centralization.evcent.tmax)
export(assortativity.nominal)
export(assortativity)
export(assortativity.degree)
export(contract.vertices)
export(eccentricity)
export(radius)
export(graph.diversity)
export(is.degree.sequence)
export(is.graphical.degree.sequence)
export(graph.bfs)
export(graph.dfs)
export(bipartite.projection.size)
export(bipartite.projection)
export(graph.bipartite)
export(graph.incidence)
export(get.incidence)
export(bipartite.mapping)
export(graph.laplacian)
export(clusters)
export(articulation.points)
export(biconnected.components)
export(maximal.cliques.count)
export(layout.star)
export(layout.grid)
export(layout.grid.3d)
export(layout.fruchterman.reingold)
export(layout.graphopt)
export(layout.drl)
export(layout.drl)
export(layout.sugiyama)
export(layout.mds)
export(layout.bipartite)
export(similarity.jaccard)
export(similarity.dice)
export(similarity.invlogweighted)
export(community.le.to.membership)
export(mod.matrix)
export(leading.eigenvector.community)
export(label.propagation.community)
export(multilevel.community)
export(optimal.community)
export(hrg.fit)
export(hrg.game)
export(hrg.dendrogram)
export(hrg.consensus)
export(hrg.predict)
export(hrg.create)
export(infomap.community)
export(graphlets)
export(graphlets.candidate.basis)
export(graphlets.project)
export(as.undirected)
export(get.stochastic)
export(dyad.census)
export(triad.census)
export(adjacent.triangles)
export(graph.maxflow)
export(dominator.tree)
export(stCuts)
export(stMincuts)
export(is.separator)
export(is.minimal.separator)
export(minimal.st.separators)
export(minimum.size.separators)
export(cohesive.blocks)
export(graph.isoclass)
export(graph.isomorphic)
export(graph.isoclass.subgraph)
export(graph.isocreate)
export(graph.isomorphic.vf2)
export(graph.count.isomorphisms.vf2)
export(graph.get.isomorphisms.vf2)
export(graph.subisomorphic.vf2)
export(graph.count.subisomorphisms.vf2)
export(graph.get.subisomorphisms.vf2)
export(graph.isomorphic.34)
export(canonical.permutation)
export(permute.vertices)
export(graph.isomorphic.bliss)
export(graph.automorphisms)
export(graph.subisomorphic.lad)
export(scgGrouping)
export(scgSemiProjectors)
export(scgNormEps)
export(is.matching)
export(is.maximal.matching)
export(maximum.bipartite.matching)
export(graph.eigen)
export(sir)
export(convex.hull)
export(revolver.ml.d)
export(revolver.probs.d)
export(revolver.ml.de)
export(revolver.probs.de)
export(revolver.ml.ade)
export(revolver.probs.ade)
export(revolver.ml.f)
export(revolver.ml.df)
export(revolver.ml.l)
export(revolver.ml.ad)
export(revolver.probs.ad)
export(revolver.ml.D.alpha)
export(revolver.ml.D.alpha.a)
export(revolver.ml.DE.alpha.a)
export(revolver.ml.AD.alpha.a.beta)
export(revolver.ml.AD.dpareto)
export(revolver.ml.AD.dpareto.eval)
export(revolver.ml.ADE.alpha.a.beta)
export(revolver.ml.ADE.dpareto)
export(revolver.ml.ADE.dpareto.eval)
export(revolver.ml.ADE.dpareto.evalf)
export(revolver.probs.ADE.dpareto)