NAMESPACE
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 import(methods)
 import(utils)
 
 importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
                    plot.igraph, igraph.to.graphNEL)
 
 
 import(BiocGenerics)
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 import(S4Vectors)
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 import(IRanges)
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 import(GenomeInfoDb)
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 import(GenomicRanges)
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 import(GenomicFeatures)
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 importFrom(Rsamtools, asBam)
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 import(GenomicAlignments)
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 importFrom(graph, nodeDataDefaults, nodeData,
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                   edgeDataDefaults, edgeNames, edgeData, edgemode)
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 importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
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 exportClasses(GeneModel, SplicingGraphs)
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 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Export S4 methods for generics not defined in SplicingGraphs
 ###
 
 exportMethods(
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     length,
     names,
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     show,
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     "[",
     "[[",
     elementLengths,
     unlist,
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     seqnames,
     strand,
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     seqinfo,
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     intronsByTranscript,
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     plot
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 )
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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 ### Export non-generic functions (and non-function symbols)
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 ###
 
 export(
     ## sgraph-methods.R:
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     slideshow,
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     ## rsgedgesByGene-methods.R:
     rsgedges, sgedges2,
     rsgraph, sgraph2,
 
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     ## bubbles-methods.R:
     ASCODE2DESC,
 
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     ## assignReads.R:
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     assignReads,
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     removeReads,
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     ## toy_data.R:
     toy_genes_gff,
     toy_reads_sam,
     toy_reads_bam,
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     toy_overlaps
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 )
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Export S4 generics defined in SplicingGraphs + export corresponding
 ### methods
 ###
 
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 export(
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     ## SplicingGraphs-class.R:
     SplicingGraphs,
 
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     ## plotTranscripts-methods.R:
     plotTranscripts,
 
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     ## sgedgesByGene-methods.R:
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     sgedgesByTranscript,
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     sgedgesByGene,
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     ## txpath-methods.R:
     txpath,
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     txweight, "txweight<-",
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     ## sgedges-methods.R:
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     sgedges,
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     sgnodes,
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     outdeg, indeg,
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     ## sgraph-methods.R:
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     sgraph,
 
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     ## rsgedgesByGene-methods.R:
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     uninformativeSSids,
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     rsgedgesByTranscript,
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     rsgedgesByGene,
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     ## bubbles-methods.R:
     bubbles,
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     ## countReads-methods.R:
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     reportReads,
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     countReads
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 )
 
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 ### Exactly the same list as above.
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 exportMethods(
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     SplicingGraphs,
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     plotTranscripts,
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     sgedgesByTranscript,
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     sgedgesByGene,
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     txpath,
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     txweight, "txweight<-",
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     sgedges,
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     sgnodes,
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     outdeg, indeg,
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     sgraph,
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     uninformativeSSids,
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     rsgedgesByTranscript,
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     rsgedgesByGene,
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     bubbles,
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     reportReads,
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     countReads
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 )
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