## ============================================================
## Import
## ============================================================
## ggplot2
import(methods)
import(BiocGenerics)
import(biovizBase)
import(grid)
import(ggplot2)
import(reshape2)
import(scales)
import(plyr)
importFrom(gridExtra, grid.arrange)
importFrom(Hmisc, bezier)
## GenomicRanges
## IRanges
importFrom(IRanges, IRanges,  disjointBins,
           matchMatrix, findOverlaps, subsetByOverlaps,
           "elementMetadata", "elementMetadata<-",
           start, width, end,  resize, 
           "values", "values<-",
           ranges, "ranges<-", 
           isTRUEorFALSE, coverage, slice,
           elementLengths,  
           reduce, punion, pgap, gaps, "%in%")

importMethodsFrom(IRanges,  split, 
                  unlist, psetdiff,
                  range, endoapply,
                  as.data.frame,
                  length, as.list,
                  "[","[<-","[[", "[[<-","$",
                  show)

importClassesFrom(IRanges, Rle, RleList, IRanges, characterORNULL)

## ## GenomicRanges
importFrom(GenomicRanges, "seqnames<-",
           seqlevels, "seqlevels<-",
           GRanges, GRangesList, Seqinfo, seqlengths, "seqlengths<-")
importMethodsFrom(GenomicRanges, ranges, "ranges<-",
                  start, end, width, "start<-", "end<-", "width<-",
                  seqnames, seqinfo, show, 
                   "elementMetadata<-", elementMetadata,
                  as.data.frame, keepSeqlevels, renameSeqlevels,
                  sort)


importClassesFrom(GenomicRanges, GRanges, GRangesList, GenomicRangesList)

## ## ## Rsamtools
importFrom(Rsamtools, ScanBamParam, scanBam, scanBamHeader,
           scanBamFlag,BamFile,
           PileupFiles, PileupParam ,
           readBamGappedAlignments)
importMethodsFrom(Rsamtools, applyPileups, path)
importClassesFrom(Rsamtools, BamFile)

## ## ## BSgenome
importClassesFrom(BSgenome, BSgenome)

## ## ## GenomicFeatures
importClassesFrom(GenomicFeatures,TranscriptDb)
importFrom(GenomicFeatures,
           transcriptsByOverlaps,
           exonsBy,
           cdsBy)

## VariantAnnotation
importClassesFrom(VariantAnnotation, VCF)
importMethodsFrom(VariantAnnotation, fixed, "fixed<-", ref, "ref<-",
                  alt, "alt<-", info, "info<-", geno, "geno<-",  readVcf) 

## rtracklayer
importMethodsFrom(rtracklayer, import)

## ============================================================
## Export
## ============================================================
exportMethods(autoplot, rescale, fortify, xlim, "xlim<-", update, reset, backup)


## geom
exportMethods(geom_chevron,
              geom_arch,
              geom_alignment,
              geom_arrow,
              geom_arrowrect,
              geom_rect,
              geom_bar,              
              geom_segment)

## stat
exportMethods(stat_aggregate,
              stat_coverage,
              stat_identity,	
              stat_mismatch, 	
              stat_stepping,
              stat_gene,
              stat_table)

## layout
exportMethods(layout_karyogram,
              layout_circle)



export(tracks,
       align.plots,
       plotFragLength,        
       plotSpliceSum,       
       plotStackedOverview,
       plotSingleChrom,
       plotGrandLinear,
       plotRangesLinkedToData)

export(theme_null, theme_alignment)

 
