import(Biobase, RCurl, XML, rJava)

importFrom("IRanges", "start<-", "end<-", "start", "end", "genome", "chrom",
           "strand")

importFrom(Biostrings, read.DNAStringSet)
importFrom(Biostrings, BString)

exportClasses("genomeSegment", "chrid",
              "trackSet", "trackSets",
              "browserSession", "browserView",
              "ucscSession", "ucscView",
              "argoSession", "argoView",
              "ucscTrackSet", "ucscTrackLine", "basicTrackLine", "wigTrackLine",
              "ucscTrackModes")

exportMethods("activeView", "activeView<-", "browseGenome",
              "browserSession", "browserView", "browserViews",
              "chrid", "close", "dataVals", "export", "export.bed",
              "export.gff", "export.gff1", "export.gff2",
              "export.gff3", "export.ucsc", "export.wig", "genome", "genome<-",
              "genomeSegment", "genomeSegment<-",
              "genomeSequence", "import", "import.bed", "import.gff",
              "import.gff1", "import.gff2", "import.gff3",
              "import.ucsc", "import.wig", "laySequence", "layTrack",
              "merge", "chrom", "chrom<-", "strand",
              "trackData", "trackSet",
              "trackSets", "tracks", "tracks<-", "ucscTable",
              "ucscTrackModes", "ucscTrackModes<-", "coerce", "initialize",
              "show", "[", "start", "start<-", "end", "end<-", "*", "/")

export("genomeBrowsers", "start", "end", "start<-", "end<-", "genome", "chrom",
       "strand")

S3method(c, genomeSegment)
