# Copyright 2012 Paolo Martini <paolo.martini@unipd.it>
#
#
# This file is part of clipper.
#
# clipper is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License
# version 3 as published by the Free Software Foundation.
#
# clipper is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public
# License along with clipper. If not, see <http://www.gnu.org/licenses/>.

import(Matrix,graph,KEGGgraph,Rcpp)

importFrom(methods, as)

importClassesFrom(Biobase, ExpressionSet)
importMethodsFrom(Biobase, exprs)

importFrom(corpcor, cov.shrink)
importFrom(qpgraph, qpIPF)
importFrom(igraph, as_ids, igraph.from.graphNEL, get.edgelist, get.all.shortest.paths, graph, as_adjacency_matrix)
# importFrom(RBGL, maxClique)
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "as.dist", "cov", "cutree", "hclust", "pchisq","pf", "qchisq", "t.test")
importFrom("gRbase", "triangulate", "rip", "moralizeMAT", "maxClique")
# import(gRbase)

export(cliqueVarianceTest, cliqueMeanTest, cliqueMixedTest, getGraphEntryGenes, getJunctionTreePaths, pathQ, clipper, prunePaths, easyClip, plotInCytoscape, nameCliques, deleteEdge, easyLook, clipperAllRoots, cliquePairedTest)

