NAMESPACE

useDynLib(rtracklayer, .registration = TRUE)

## ============================================================
## Import
## ============================================================

import(methods)
import(BiocGenerics)
import(zlibbioc)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### base packages
###

importFrom("stats", offset, setNames)
importFrom("utils", count.fields, URLencode, browseURL,
           download.file, read.table, read.csv, type.convert, write.table,
           packageVersion, strcapture)
importFrom("tools", file_path_as_absolute, file_ext, file_path_sans_ext)
importFrom("grDevices", col2rgb, rgb)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Non-bioconductor packages
###

importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse, xmlTreeParse,
           xmlInternalTreeParse, parseURI, newXMLNode, xmlChildren,
           addChildren, removeChildren, readHTMLTable)
importMethodsFrom("XML", saveXML)

importFrom("curl", curl_unescape)

importFrom("httr", GET, HEAD, POST, config, user_agent, set_cookies, content,
           upload_file)

import(restfulr)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Bioconductor packages
###

import(S4Vectors)
import(XVector)
import(GenomeInfoDb)
import(IRanges)
import(GenomicRanges)
import(BiocIO)

importFrom("Biostrings", get_seqtype_conversion_lookup, writeXStringSet,
           DNAStringSet, DNA_BASES, DNA_ALPHABET, alphabetFrequency,
           reverseComplement, uniqueLetters)
importMethodsFrom("Biostrings", masks, "masks<-", getSeq)
importClassesFrom("Biostrings", DNAStringSet, XStringSet)

importFrom("Rsamtools", indexTabix, bgzip, TabixFile, index)
importMethodsFrom("Rsamtools", ScanBamParam, asBam, headerTabix, isOpen,
                  scanTabix)
importClassesFrom("Rsamtools", RsamtoolsFile, TabixFile, BamFile)

importMethodsFrom("GenomicAlignments", readGAlignments, cigar,
                  last, readGAlignmentPairs)
importClassesFrom("GenomicAlignments", GAlignments)

## ============================================================
## Export
## ============================================================

exportClasses(BrowserSession, BrowserView, BrowserViewList,
              UCSCSession, UCSCView,
              UCSCData, TrackLine, BasicTrackLine, GraphTrackLine,
              Bed15TrackLine, UCSCTrackModes, BigWigSelection,
              BigBedSelection, UCSCSchema, Quickload, QuickloadGenome,
              TrackHub, TrackHubGenome, Track, TrackContainer)

## File classes
exportClasses(RTLFile, RTLFileList, GFFFile, UCSCFile, BEDFile,
              WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File,
              BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile,
              BigWigFileList, BigBedFile, TwoBitFile, BEDPEFile)

exportMethods(activeView, "activeView<-", blocks, browseGenome,
              browserSession, "browserSession<-",
              browserView, browserViews,
              close, export, export.bed, export.bed15,
              export.bedGraph, export.gff, export.gff1, export.gff2,
              export.gff3, export.ucsc, export.wig, export.bw,
              export.bb, export.2bit,
              import, import.bed, import.bed15, import.bedGraph,
              import.gff, import.gff1, import.gff2, import.gff3,
              import.ucsc, import.wig, import.bw, import.chain,
              import.2bit, import.bb,
              exportToTabix,
              "track<-",
              track, trackNames, "trackNames<-", getTable, hubUrl, "hubUrl<-",
              tableNames, trackName, "trackName<-",
              tableName, "tableName<-",
              ucscTrackModes, "ucscTrackModes<-",
              ucscSchema,
              coerce, initialize,
              show, summary, "[", ucscTableQuery,
              genome, "genome<-", chrom, "chrom<-", range, "range<-",
              visible, "visible<-",
              liftOver, offset, reversed, nrow,
              referenceSequence, "referenceSequence<-",
              asBED, asGFF,
              split, fileFormat,
              hub, "hub<-", shortLabel, "shortLabel<-", longLabel, "longLabel<-",
              genomesFile, "genomesFile<-", email, "email<-", descriptionUrl,
              "descriptionUrl<-", genomeField, "genomeField<-", getTracks , writeTrackHub,
              trackField, "trackField<-", genomeInfo, "genomeInfo<-",
              ## from IRanges
              start, end, "start<-", "end<-",
              score, "score<-",
              as.data.frame, space, mcols,
              ## from GenomicRanges
              strand, seqinfo, "seqinfo<-",
              ## from BSgenome
              organism, releaseDate, getSeq
              )

export(genomeBrowsers, start, end, strand, "start<-", "end<-", width, "width<-",
       ranges, values, GenomicData, GenomicSelection,
       score, "score<-", as.data.frame, space,
       ucscGenomes, ucscTables,
       readGFFPragmas, sniffGFFVersion, GFFcolnames, readGFF, readGFFAsGRanges,
       BigWigSelection, BigBedSelection,
       GRangesForUCSCGenome, GRangesForBSGenome,
       summary, seqinfo, genome, "genome<-", Genome,
       uri, Quickload, quickload, QuickloadGenome,
       organism, releaseDate, mcols, TrackHub, trackhub, TrackHubGenome,
       Track, TrackContainer, wigToBigWig,
       SeqinfoForBSGenome, SeqinfoForUCSCGenome, resource, path,
       FileForFormat, cleanupBigWigCache, cleanupBigBedCache, viewURL)

export(GFFFile, UCSCFile, BEDFile, WIGFile,
       ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile,
       BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile,
       BEDPEFile, BigBedFile)