/NAMESPACE

  1############################################################
  2## Import
  3############################################################
  4import(methods)
  5importFrom(utils, head, tail)
  6importFrom(stats, start, end, update, aggregate)
  7import(objectSignals)
  8import(objectProperties)
  9import(objectWidgets)
 10import(objectWidgetsQt)
 11importFrom(plumbr, mutaframe, mutalist)
 12import(qtbase)
 13import(qtpaint)
 14import(scales)
 15importFrom(BiocGenerics, cbind, rbind, unique,
 16           lapply, sapply, setdiff, Reduce)
 17## importClassesFrom(BiocGenerics, AsIs)
 18import(biovizBase)
 19## Biobase
 20importClassesFrom(Biobase, AssayData)
 21
 22##IRanges
 23## importClassesFrom(IRanges, IRanges, Rle)
 24importFrom(IRanges, IRanges,  disjoin, disjointBins,
 25           "elementMetadata", "elementMetadata<-",
 26           start, width, end,  mid, resize, 
 27           "start<-", "width<-", "end<-", "values", "values<-",
 28           ranges, "ranges<-", "metadata", "metadata<-", 
 29           isTRUEorFALSE, coverage, slice, viewWhichMins, viewWhichMaxs,
 30           viewMins, viewMaxs, viewSums, viewMeans, runValue, runLength, reduce,
 31           punion, pgap)
 32
 33importMethodsFrom(IRanges,
 34                  unlist,setdiff, Rle,
 35                  Reduce,
 36                  as.data.frame,
 37                  length, as.vector,
 38                  "[","[<-","[[", "[[<-","$",
 39                  "%in%", show, as.list,
 40                  aggregate, append,
 41                  colnames, "colnames<-", lapply, sapply)
 42
 43importClassesFrom(IRanges, Annotated, List, Vector, SimpleList,
 44                  characterORNULL, functionORNULL)
 45
 46
 47## ## GenomicRanges
 48############################################################
 49importFrom(GenomicRanges, "seqnames<-","strand<-", GRanges, GRangesList, Seqinfo,
 50           seqlengths, "seqlengths<-", keepSeqlevels)
 51importMethodsFrom(GenomicRanges, ranges, "ranges<-",
 52                  start, end, width, "start<-", "end<-", "width<-",
 53                  seqnames, strand, seqinfo, show, seqlevels,
 54                   "elementMetadata<-", elementMetadata,
 55                  as.data.frame)
 56importClassesFrom(GenomicRanges, GRanges, GenomicRanges, Seqinfo)
 57## GenomicFeatures
 58importClassesFrom(GenomicFeatures,TranscriptDb)
 59
 60
 61## ## MutableRanges
 62import(MutableRanges)
 63## importClassesFrom(MutableRanges, MutableGRanges,
 64##                   OverlapTypeSingleEnum)
 65
 66## importFrom(MutableRanges, MutableGRanges)
 67
 68## importMethodsFrom(MutableRanges, 
 69##                   elementMetadataChanged, rangesChanged)
 70## BSgenome
 71importClassesFrom(BSgenome, BSgenome)
 72importMethodsFrom(BSgenome, getSeq)
 73
 74## rtracklayer
 75importClassesFrom(rtracklayer, BrowserView)
 76importFrom(rtracklayer, browserSession, genome, "genome<-",
 77           ucscTableQuery, tableNames, getTable, GenomicData,
 78           "track<-", GRangesForUCSCGenome, browserView,
 79           ucscGenomes, "tableName<-")
 80
 81## Rsamtools
 82importFrom(Rsamtools, ScanBamParam, scanBam, scanBamHeader,
 83           PileupFiles, PileupParam , countBam, BamFile)
 84importMethodsFrom(Rsamtools, applyPileups)
 85
 86
 87############################################################
 88## Export
 89############################################################
 90exportMethods(unlist,lapply,
 91              length,
 92              print)
 93              ## icons,
 94              ## viewInBrowser,
 95              ## visnabGUI,
 96              ## range,
 97              ## "range<-",
 98              ## selectedRangesModel,
 99              ## "selectedRangesModel<-",
100              ## geom,
101              ## "geom<-",
102              ## aes)
103
104
105## ## Constructor
106export(GraphicPars,
107       ## IntervalView,
108       ## CircularView,
109       ## AlignmentView,
110       CoverageView)
111       ## SeqView,
112       ## StackedView,
113       ## TracksView,
114       ## TxdbView,
115       ## VisnabViewList,
116       ## VisnabProject)-
117
118## exportClasses("numericORNULL",
119##               "characterORNULL",
120##               "functionORNULL", 
121##               "logicalORNULL",
122##               "Theme") 
123
124exportClasses(ColorEnum, GlyphEnum)
125## GUI
126##exportClasses(SearchBar)
127## exportMethods(SearchBar)
128## export(SearchBar, ControlPanel, SimpleViewer,
129##        setGraphicPars)
130
131## ## utils method
132## export("getIdeogram")
133
134## for temporary
135exportPattern("^[^\\.]")
136