/NAMESPACE
#! | 136 lines | 116 code | 20 blank | 0 comment | 0 complexity | bcc02b9fddbf9658fedafc356f5aca93 MD5 | raw file
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