NAMESPACE

import(Rgraphviz)
importClassesFrom(Matrix, dgCMatrix)
importMethodsFrom(Matrix, '%*%', '+', '-')
importClassesFrom(graph, graphNEL)
importFrom(igraph, graph.laplacian, graph.data.frame, get.all.shortest.paths, E, V, is.igraph,
is.directed, list.edge.attributes, get.edges, get.adjlist)
importFrom(graph, nodes, edgeWeights)
importFrom(DBI, dbConnect, dbDisconnect, dbGetQuery, dbReadTable)


exportClasses(rwrParams, variantFilter, annotatedIGraph, graphDispParams, priorDbParams, variantPriorResult, rwrParams)
export(saveGraph, loadGraph)
export(makeGraphDispParams, fileName, height, width)
export(transformGraph, nodeWeightCol)
export(makeVariantFilter)
exportPattern("^filter")
export(makeVariantPriorResult)
exportPattern("^get")

export(reconcile.sample.name, get.protein.protein.graph, get.sample.variants, filter.variant.annots, get.hit.prots, get.sample.overlays, retrieve.param.query,
run.prioritization.patient, run.protocol, random.walk, collapse.nodes.genes)
export(process.node.annot, add.in.missing.nodes, protein.list.to.gene, draw.graph.variantPriorResult, draw.graph, make.target.graph, get.graph.sp, makeRwrParams)

export(patVarID, "patVarID<-",patVarID,"patVarID<-",additionalIDs,"additionalIDs<-",annotQuery,"annotQuery<-",combScoreName,"combScoreName<-",coreID,"coreID<-",
hitQuery,"hitQuery<-",idTable,"idTable<-",matrixQuery,"matrixQuery<-",patientFilterCol,"patientFilterCol<-",patientFreqCol,"patientFreqCol<-",patientOverlay,"patientOverlay<-",
possibleIdCols,"possibleIdCols<-",queryLabel,"queryLabel<-",reconciledIdCol,"reconciledIdCol<-",rwrParamsObj,"rwrParamsObj<-",sampleIdCol,"sampleIdCol<-",seedLabel,
"seedLabel<-",getSummarizationLevel,summaryID,"summaryID<-",summaryMap,"summaryMap<-",variantFilterObj,"variantFilterObj<-",variantQuery,"variantQuery<-",variantTypeCol,
"variantTypeCol<-",nodeWeightCol,show,transformGraph,"transformGraph<-",verbLevel,"verbLevel<-",queryParams,"queryParams<-",scoreSummaryFunc,"scoreSummaryFunc<-", annotation,
"annotation<-")

export(fileName,"fileName<-", collapseChar, "collapseChar<-", defaultBorder, "defaultBorder<-", defaultColor, "defaultColor<-", hitColors, "hitColors<-", labelFuncList,
"labelFuncList<-", labelSep,"labelSep<-", maxPlotHits, "maxPlotHits<-", maxPlotVars, "maxPlotVars<-", nameTextSep, "nameTextSep<-", nodeCombinationFunc, "nodeCombinationFunc<-",
plotFunc, "plotFunc<-", queryColor, "queryColor<-", shapeFunc, "shapeFunc<-", styleFunc, "styleFunc<-", height, "height<-", show, width, "width<-")