NAMESPACE

useDynLib(TFBSTools, .registration = TRUE)


### -----------------------------------------------------------------
### Import S4 classes defined in other packages
###
importClassesFrom(S4Vectors, Annotated, Vector, SimpleList, List, DataFrame)
importClassesFrom(Biostrings, DNAStringSet, PairwiseAlignments, XStringViews)
importClassesFrom(GenomicRanges, GRanges, GRangesList)
importClassesFrom(methods, ANY, character, integer, missing)
importClassesFrom(CNEr, Axt)
import(BiocGenerics)


### -----------------------------------------------------------------
### Import S4 methods defined in other packages
###
importMethodsFrom(Biostrings, reverseComplement, matchPWM, maxScore, minScore, 
                  consensusMatrix, PairwiseAlignments, pattern, consensusMatrix)
importMethodsFrom(DBI, dbGetQuery)
importMethodsFrom(RSQLite, dbConnect, dbDisconnect)
importMethodsFrom(XVector, subseq)
importMethodsFrom(GenomicRanges, seqnames, strand, "strand<-", 
                  findOverlaps, reduce)
importMethodsFrom(rtracklayer, import.chain, liftOver)
importMethodsFrom(BSgenome, getSeq)
importMethodsFrom(methods, initialize, show)
importMethodsFrom(S4Vectors, isConstant, elementNROWS, Rle, window, showAsCell)
importMethodsFrom(IRanges, subject, ranges, "ranges<-",
                  Views, start, end, findOverlaps, width, which, pintersect)
importMethodsFrom(CNEr, querySeqs, targetSeqs, targetRanges, queryRanges)
importMethodsFrom(DirichletMultinomial, fitted)
importMethodsFrom(GenomeInfoDb, seqinfo)

### -----------------------------------------------------------------
### Import ordinary functions, variables in other packages
importFrom(seqLogo, seqLogo, makePWM)
importFrom(Biostrings, unitScale, PWMscoreStartingAt, 
                       DNAStringSet, DNA_BASES, DNA_ALPHABET, readDNAStringSet, 
                       readAAStringSet, writeXStringSet, IUPAC_CODE_MAP,
                       DNAString)
importFrom(caTools, runmean)
importFrom(GenomicRanges, GRanges, GRangesList)
importFrom(methods, is, new, as, slot)
importFrom(RSQLite, SQLite)
importFrom(IRanges, IRanges)
importFrom(gtools, rdirichlet)
importFrom(BiocParallel, MulticoreParam, bpmapply)
importFrom(DirichletMultinomial, dmn, laplace, mixturewt)
importFrom(TFMPvalue, TFMsc2pv)
importFrom(S4Vectors, DataFrame, queryHits, subjectHits)
importFrom(XML, xmlParse, xmlToList)
importFrom(grid, grid.newpage, plotViewport, dataViewport, 
           grid.xaxis, grid.polygon, pushViewport, grid.text, popViewport,
           unit, gpar)
importFrom(Biobase, rowMax, rowMin)
importFrom("graphics", "par")
importFrom("stats", "runif", "setNames")
importFrom("utils", "write.table")
importFrom(parallel, mclapply)

### -----------------------------------------------------------------
### Export S4 classes defined in TFBSTools
###
exportClasses(PFMatrix, PWMatrix, ICMatrix,
  PFMatrixList, PWMatrixList, ICMatrixList,
  SiteSet, SiteSetList, SitePairSet, SitePairSetList,
  MotifSet
  #PairwiseAlignmentTFBS
  )

### -----------------------------------------------------------------
### Export non-generic functions
###
export(
  ## AllClasses.r
  PFMatrix, PFMatrixList,
  ICMatrix, ICMatrixList,
  PWMatrix, PWMatrixList,
  MotifSet,
  SitePairSetList, SitePairSet,
  SiteSet, SiteSetList,
  TFFMFirst, TFFMDetail, 

  ## util-methods.r
  shannon.entropy,
  IUPAC2Matrix,
  sampleRanges,

  ## TFFMseqLogo.R
  
  ## Wrappers-methods.R
  parseMEMEOutput,

  ## IO.R
  readXMLTFFM
)

### -----------------------------------------------------------------
### Export S4 methods for generics not defined in TFBSTools
###
exportMethods(
  ## XMatrix-methods.r
  length,
  ncol,
  dim,
  reverseComplement,
  
  ## XMatrixList-methods.r
  showAsCell,
  
  ## SiteSet-methods.r
  start, end,

  ## coercion-methods.r
  as.matrix, as.data.frame,

  # XMatrix-methods.r
  colSums,
  rowSums,

  ## Motif-methods.r
  consensusMatrix
)

### -----------------------------------------------------------------
### Export S4 generics defined in TFBSTools + export corresponding methods
###
export(
  ## DB-methods.r
  storeMatrix,
  getMatrixSet,
  getMatrixByID, getMatrixByName,
  deleteMatrixHavingID,
  initializeJASPARDB,

  ## JASPAR.R
  makeFlatFileDir, readJASPARMatrix,
  
  ## AllGenerics.r
  ID, 
  name, 
  matrixClass, 
  Matrix,
  "Matrix<-",
  bg, 
  tags,
  matrixType,
  XMatrixList,
  #alignments,

  # XMatrix-methods.r
#colSums,
#  rowSums,

  ## PWM-methods.r
  toPWM,
  searchSeq,
  searchAln,
  searchPairBSgenome,
  PWMSimilarity,

  ## ICM-methods.r
  toICM,
  seqLogo,
  totalIC,

  ## SiteSet-methods.r
  writeGFF3, writeGFF2,
  relScore,
  views,
  pvalues,
  toGRangesList,

  ## PairwiseAlignment-methods.r
  calConservation,
  #doSiteSearch

  ## PFM-methods
  PFMSimilarity,
  permuteMatrix,

  ## DirichletMixture.r
  dmmEM, rPWMDmm,

  ## Wrappers-methods.r
  runMEME,
  sitesSeq,
 
  ## TFFM.R
  getEmissionProb, getPosProb

)