#Generated by codetoolsBioC version 0.0.16
#Timestamp: Tue Feb 14 10:11:41 2012

#Imports: AnnotationDbi, Biobase, BiocGenerics, biomaRt, GenomicRanges,
#         graphics, grDevices, grid, IRanges, lattice, methods, RColorBrewer,
#         rtracklayer, stats, utils

import(methods)

importClassesFrom(biomaRt, Mart)

importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)

importClassesFrom(GenomicRanges, GRanges)

importClassesFrom(BSgenome, BSgenome, MaskedBSgenome)

importClassesFrom(GenomicFeatures, "TranscriptDb")

importClassesFrom(IRanges, IRanges, NormalIRanges)

importClassesFrom(XVector, GroupedIRanges)


importClassesFrom(rtracklayer, UCSCData)

importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)

importMethodsFrom(Biobase, rowMedians)

importMethodsFrom(BiocGenerics, cbind, duplicated, eval, intersect, lapply,
                  mapply, order, paste, pmax, pmin, rbind, sapply, setdiff,
                  table, tapply, unique)

importMethodsFrom(BSgenome, providerVersion)

importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)

importMethodsFrom(GenomicRanges, "elementMetadata<-", genome, "genome<-", mcols, "mcols<-",
                  seqlengths, seqnames, seqlevels, seqinfo, strand, "strand<-",
                  seqnameStyle, shift)

importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, as.vector,
                  "colnames<-", coverage, diff, disjointBins, end, "end<-", range,
                  findOverlaps, findRun, gsub, ifelse, "%in%", levels, match,
                  mean, ncol, nrow, queryHits, ranges, "ranges<-", reduce, rev,
                  Rle, rownames, "rownames<-", runmean, runValue, "runValue<-",
                  score, sort, split, start, "start<-", sub, subjectHits,
                  substring, t, tolower, unlist, values, "values<-", which,
                  which.max, width, "width<-", elementMetadata, endoapply,
                  elementLengths, overlapsAny)


importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-", track,
                  ucscTableQuery, trackNames, tableNames, import, import.gff,
                  import.gff1, import.gff2, import.gff3, import.2bit, import.bed15,
                  import.bw, import.ucsc, import.bed, import.bedGraph, import.chain,
                  import.wig, seqinfo)

importMethodsFrom(Biostrings, consensusMatrix)


importFrom(Biobase, listLen, rowMax, rowMin)

importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement, readDNAStringSet, DNA_ALPHABET, stackStrings)

importFrom(BiocGenerics, getObjectSlots)

importFrom(biomaRt, getBM, useMart)

importFrom(GenomicRanges, GRanges, renameSeqlevels)

importFrom(Rsamtools, scanBamFlag, scanBamHeader, scanBam, ScanBamParam, scanFaIndex, scanFa, BamFile, scanBamWhat, bamWhich)

importFrom(graphics, par)

importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
           hsv, rgb2hsv)

importFrom(grid, convertHeight, convertWidth, convertX, convertY,
           current.transform, current.viewport, current.vpTree, dataViewport,
           downViewport, gpar, grid.circle, grid.lines, grid.newpage,
           grid.polygon, grid.rect, grid.segments, grid.text, grid.yaxis,
           popViewport, pushViewport, stringHeight, stringWidth, unit,
           upViewport, viewport)

importFrom(IRanges, IRanges, DataFrame)

importFrom(XVector, subseq)

importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
           panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
           trellis.par.get)

importFrom(matrixStats, colMaxs)

importFrom(latticeExtra, panel.xyarea, panel.horizonplot)


importFrom(RColorBrewer, brewer.pal)

importFrom(rtracklayer, GenomicData, ucscGenomes, browserSession, BigWigFile, FastaFile, TwoBitFile)

importFrom(stats, loess.smooth)

importFrom(biovizBase, getBioColor)

importFrom(utils, assignInNamespace, browseURL, head, write.table)

importFrom(GenomicAlignments, extractAlignmentRangesOnReference, sequenceLayer)

###

export(".chrName",
       ".doCache",
       "AlignedReadTrack",
       "AlignmentsTrack",
       "AnnotationTrack",
       "DetailsAnnotationTrack",
       "BiomartGeneRegionTrack",
       "DataTrack",
       "DisplayPars",
       "SequenceTrack",
       "OverlayTrack",
       "drawGD",
       "GeneRegionTrack",
       "GenomeAxisTrack",
       "HighlightTrack",
       "IdeogramTrack",
       "UcscTrack",
       "addScheme",
       "as.list",
       "availableDefaultMapping",
       "availableDisplayPars",
       "clearSessionCache",
       "exportTracks",
       "getScheme",
       "plotTracks")

exportClasses("AlignedReadTrack",
              "AlignmentsTrack",
              "AnnotationTrack",
              "DetailsAnnotationTrack",
              "BiomartGeneRegionTrack",
              "DataTrack",
              "DisplayPars",
	      "GdObject",
              "GeneRegionTrack",
              "GenomeAxisTrack",
              "IdeogramTrack",
              "ImageMap",
	      "NumericTrack",
	      "RangeTrack",
              "SequenceTrack",
	      "StackedTrack",
              "HighlightTrack",
              "OverlayTrack")

exportMethods("[",
              "as.list",
              "chromosome",
              "chromosome<-",
              "coerce",
              "consolidateTrack",
              "coords",
              "coverage",
              "displayPars",
              "displayPars<-",
              "elementMetadata<-",
              "end",
              "end<-",
              "exon",
              "exon<-",
              "feature",
              "feature<-",
              "gene",
              "gene<-",
              "genome",
              "genome<-",
              "getPar",
              "group",
              "group<-",
              "head",
              "identifier",
              "identifier<-",
              "imageMap",
              "initialize",
              "length",
              "max",
              "min",
              "names",
              "names<-",
              "position",
              "range",
              "ranges",
              "score",
              "seqnames",
              "seqlevels",
              "seqinfo",
              "setPar",
              "split",
              "stacking",
              "stacking<-",
              "stacks",
              "start",
              "start<-",
              "strand",
              "strand<-",
              "subseq",
              "subset",
              "symbol",
              "symbol<-",
              "tags",
              "tail",
              "transcript",
              "transcript<-",
              "values",
              "values<-",
              "width",
              "width<-")