#############################
##
## IMPORT
##
#############################

##For S4 usage
import("methods")

##Package used in HiTC
importFrom("graphics", "plot", "image", "abline", "axis", "text")

importFrom("grDevices", "col2rgb")

importMethodsFrom("Biostrings", "detail")
importMethodsFrom("ShortRead", "id")

importMethodsFrom("girafe", "reduce", "plot", "export", "id<-")
importFrom("girafe", "fracOverlap")

importClassesFrom("genomeIntervals", "Genome_intervals", "Genome_intervals_stranded")
importMethodsFrom("genomeIntervals", "strand", "strand<-", "seq_name", "seq_name<-")

#############################
##
## EXPORT
##
#############################

##Export functions and generics
export("binningC", "discretize", "exportC", "export.my5C", "extractRegion", "getExpectedCounts", "HTCexp", "importC", "import.my5C", "mapC", "plot", "intervalsDist", "CQC", "readBED", "removeIntervals", "setIntervalScale", "show")

##Export classes
exportClasses("HTCexp")

##Export Methods
exportMethods("detail","divide", "intdata", "intdata<-", "isBinned", "isIntraChrom", "y_intervals", "y_intervals<-", "id", "id<-", "normPerReads", "normPerExpected", "plot", "x_intervals", "x_intervals<-", "seq_name", "strand", "substract")

