R/AllClasses-Base.R

In ShortRead: FASTQ input and manipulation

## .STRAND_LEVELS needs to be early, to be used in class
## prototypes. C-level code retrieves this value.
## readAligned,type=MAQMap depends on this ordering.
.STRAND_LEVELS <- levels(strand())
.toStrand_Solexa <- function(x)
    factor(.STRAND_LEVELS[match(x, c("F", "R"))],
           levels=.STRAND_LEVELS)

.srValidity <- function(object) TRUE

setGeneric(".srValidity")

## Virtual base classes

setClass(".ShortReadBase")

## .SRUtil: SRError / SRList / SRVector / SRFilter

setClass(".SRUtil",
         representation=representation("VIRTUAL"))

setClass("SRError", contains=".SRUtil",
         representation=representation(
           .type="character",
           .message="character"),
         prototype=prototype(
           .type="Unspecified",
           .message="unknown error"),
         validity=.srValidity)

setClass("SRWarn", contains=".SRUtil",
         representation=representation(
           .type="character",
           .message="character"),
         prototype=prototype(
           .type="Unspecified",
           .message="unknown warning"),
         validity=.srValidity)

setClass("SRList", contains=".SRUtil",
         representation=representation(
           .srlist="list"),
         prototype=prototype(
           .srlist=list()))

setClass("SRVector", contains="SRList",
         representation=representation(
           vclass="character"),
         prototype=prototype(
           vclass=NA_character_),
         validity=.srValidity)

setClass("SRFilter",
         contains=c("function", ".SRUtil"),
         representation=representation(
           name="ScalarCharacter"),
         validity=.srValidity)

setClass("SRFilterResult",
         contains=c("logical", ".SRUtil"),
         representation=representation(
           name="ScalarCharacter",
           stats="data.frame"))

## Intensity

setClass("IntensityMeasure", contains=".ShortReadBase",
         representation=representation("VIRTUAL"))

setClass("IntensityInfo", contains=".ShortReadBase",
         representation=representation("VIRTUAL"))

setClass("Intensity", contains=".ShortReadBase",
         representation=representation(
           .hasMeasurementError="ScalarLogical",
           readInfo="IntensityInfo",
           intensity="IntensityMeasure",
           measurementError="IntensityMeasure",
           "VIRTUAL"),
         prototype=prototype(
           .hasMeasurementError=mkScalar(FALSE)),
         validity=.srValidity)

## Intensity, implementation

setClass("ArrayIntensity",
         contains=c("array", "IntensityMeasure"),
         prototype=prototype(array(0, c(0, 0, 0))))

ArrayIntensity <-
    function(intensity=array(0, c(0, 0, 0)), ...)
{
    new("ArrayIntensity", intensity, ...)
}

setClass("SolexaIntensityInfo",
         ## AnnotatedDataFrame as prototype does not work, r46984.
         ## .init is a work-around to identify user-constructed
         ## objects that should be valid; used in .srValidity-method
         contains=c("AnnotatedDataFrame", "IntensityInfo"),
         representation=representation(.init="ScalarLogical"),
         prototype=prototype(.init=mkScalar(FALSE)),
         validity=.srValidity)

SolexaIntensityInfo <-
  function(lane=integer(0), tile=integer(0)[seq_along(lane)],
           x=integer(0)[seq_along(lane)],
           y=integer(0)[seq_along(lane)])
{
    new("SolexaIntensityInfo",
        data=data.frame(
          lane=lane, tile=tile, x=x, y=y),
        varMetadata=data.frame(
          labelDescription=c(
            "Solexa lane nubmer",
            "Solexa tile nubmer",
            "Tile x coordinate",
            "Tile y coordinate")),
        .init=mkScalar(TRUE))
}

setClass("SolexaIntensity", contains="Intensity",
         prototype=prototype(
           readInfo=SolexaIntensityInfo(),
           intensity=ArrayIntensity(),
           measurementError=ArrayIntensity()),
         validity=.srValidity)

setClass("RtaIntensity", contains="SolexaIntensity")

## QualityScore

setClass("QualityScore", contains=".ShortReadBase",
         representation=representation("VIRTUAL"))

setClass("NumericQuality", contains="QualityScore",
         representation=representation(
           quality="numeric"))

NumericQuality <- function(quality=numeric(0)) { # used below
    new("NumericQuality", quality=quality)
}

setClass("IntegerQuality", contains="NumericQuality",
         representation=representation(
           quality="integer"))

setClass("MatrixQuality", contains="QualityScore",
         representation=representation(
           quality="matrix"))

setClass("FastqQuality", contains="QualityScore",
         representation=representation(
           quality="BStringSet"),
         prototype=prototype(
           quality=BStringSet(character(0))))

setClass("SFastqQuality", contains="FastqQuality") # Solexa variant

## ShortRead / ShortReadQ

setClass("ShortRead", contains=".ShortReadBase",
         representation=representation(
           sread="DNAStringSet",
           id="BStringSet"),
         prototype=prototype(
           sread=DNAStringSet(character(0)),
           id=BStringSet(character(0))),
         validity=.srValidity)

setClass("ShortReadQ", contains="ShortRead",
         representation=representation(
           quality="QualityScore"),
         prototype=prototype(
           quality=NumericQuality()),
         validity=.srValidity)

## ExperimentPath (base class for experimental data paths)

setClass("ExperimentPath", contains = c(".ShortReadBase"),
         representation = representation(
           basePath="character"),
         prototype = prototype(
           basePath=NA_character_),
         validity = .srValidity)

## SRSet (base class for datasets)

setClass("SRSet", contains = ".ShortReadBase",
         representation = representation(
           sourcePath="ExperimentPath", # for lazy loading
           readIndex="integer", # for tracking subsets and sorting
           readCount="integer", # counts of reads in each sample
           phenoData="AnnotatedDataFrame", # experimental design
           readData="AnnotatedDataFrame"), # arbitrary read annotations
         prototype = prototype(
           sourcePath=new("ExperimentPath"),
           readIndex=integer(0),
           readCount=integer(0),
           phenoData=new("AnnotatedDataFrame"),
           readData=new("AnnotatedDataFrame")),
         validity = .srValidity)

## AlignedRead: AlignedDataFrame

setClass("AlignedDataFrame", contains="AnnotatedDataFrame",
         prototype=prototype(
           new("AnnotatedDataFrame",
               dimLabels=c("readName", "alignColumn"))),
         validity=.srValidity)

setClass("AlignedRead", contains="ShortReadQ",
         representation=representation(
           chromosome="factor",
           position="integer",
           strand="factor",
           alignQuality="QualityScore",
           alignData="AlignedDataFrame"),
         prototype=prototype(
           strand=factor(levels=.STRAND_LEVELS),
           alignQuality=NumericQuality()),
         validity=.srValidity)

## .Solexa

setClass(".Solexa", contains=".ShortReadBase",
         representation=representation("VIRTUAL"))

setClass("SolexaPath", contains=c("ExperimentPath", ".Solexa"),
         representation=representation(
           dataPath="character",
           scanPath="character",
           imageAnalysisPath="character",
           baseCallPath="character",
           analysisPath="character"),
         prototype=prototype(
           scanPath=NA_character_,
           dataPath=NA_character_,
           imageAnalysisPath=NA_character_,
           baseCallPath=NA_character_,
           analysisPath=NA_character_),
         validity=.srValidity)

setClass("SolexaSet", contains=".Solexa",
         representation=representation(
           solexaPath="SolexaPath",
           laneDescription="AnnotatedDataFrame"),
         prototype=prototype(
           solexaPath=new("SolexaPath"),
           laneDescription=new("AnnotatedDataFrame",
             data=data.frame(1:8)[,FALSE],
             dimLabels=c("laneNames", "laneColumns"))),
         validity=.srValidity)

### .Roche

setClass(".Roche", contains=".ShortReadBase",
         representation=representation("VIRTUAL"))

setClass("RochePath", contains=c("ExperimentPath", ".Roche"),
         representation=representation(
           readPath="character",
           qualPath="character"),
         prototype=prototype(
           readPath=NA_character_,
           qualPath=NA_character_),
         validity=.srValidity)

setClass("RocheSet", contains=c("SRSet", ".Roche"),
         representation=representation(
           sourcePath="RochePath"),
         prototype=prototype(
           sourcePath=new("RochePath")),
         validity=.srValidity)

## QA

setClass(".QA", contains=c("SRList", ".ShortReadBase"),
         representation=representation("VIRTUAL"))

setClass("ShortReadQQA", contains=".QA")

setClass("FastqQA", contains="ShortReadQQA") # synonym

setClass("SolexaExportQA", contains=".QA")

setClass("SolexaRealignQA", contains=".QA")

setClass("MAQMapQA", contains=".QA")

setClass("BowtieQA", contains=".QA")

## Snapshot

setClass("SnapshotFunction",
    representation=representation(
        reader="function", 
        viewer="function", 
        limits="integer"))

setClass("SnapshotFunctionList", "SimpleList",
         prototype=prototype(elementType="SnapshotFunction"))

setOldClass("trellis")

.SpTrellis <-
    setRefClass("SpTrellis",
                fields=list(trellis="trellis", .debug_enabled="logical"))

.Snapshot <-
    setRefClass("Snapshot",
      fields=list(
        .debug="function", .auto_display="logical",
        ## ranges
        .range="GRanges", .orig.range="GRanges", .zin="logical", 
        .pright="logical",
        ## data
        .data="data.frame", .data_dirty="logical",
        .initial_functions="SnapshotFunctionList",
        .current_function="character", .using_initial_functions="logical",
        ## more-or-less public
        ## annotation track 
        files="BamFileList", functions="SnapshotFunctionList",
        view="SpTrellis", annTrack="ANY", ignore.strand="logical",
        fac="character"))

## ShortReadFile -- methods elsewhere

.ShortReadFile_g <- setRefClass("ShortReadFile",
    fields=list(con="ANY", path="character"),
    methods=list(
      msg = function(txt) {
          "display 'txt' with status information as a message()"
          s <- status(update=TRUE)
          message(txt, " ", paste(names(s), s, sep="=", collapse=" "))
      },
      status=function(update=FALSE) {},
      show = function() {
          cat("class:", class(.self), "\n")
          cat(Rsamtools:::.ppath("path", path))
          cat("isOpen:", isOpen(.self), "\n")
      }))

.FastqFile_g <-
    setRefClass("FastqFile", contains="ShortReadFile")

.FastqFileReader_g <- setRefClass("FastqFileReader",
    contains="FastqFile",
    fields = list(
      reader = "function", readerBlockSize="integer",
      .status = "integer", sampler = "externalptr",
      verbose = "logical"),
    methods = list(
      yield = function(...) {
          stop("'yield' not implemented for class '",
               class(.self), "'")
      },
      show = function() {
          cat("class:", class(.self), "\n")
          nm <- tryCatch({
              basename(summary(.self$con)$description)
          }, error=function(err) {
              "closed"
          })
          cat("file:", nm, "\n")
          s <- .self$status()
          cat("status:", paste(names(s), s, sep="=", collapse=" "), "\n")
      }))

.FastqStreamer_g <- setRefClass("FastqStreamer",
    contains="FastqFileReader",
    fields = list(
      skips="integer", adds = "integer", ith = "integer",
      recycle = "logical"))

.FastqSampler_g <- setRefClass("FastqSampler",
    contains="FastqFileReader",
    fields = list(
      ordered = "logical"))

setClass("FastqFileList", contains="RsamtoolsFileList",
    prototype=prototype(elementType="FastqFile"))

setClass("FastqSamplerList", contains="FastqFileList",
         prototype=prototype(elementType="FastqSampler"))

setClass("FastqStreamerList", contains="FastqFileList",
         prototype=prototype(elementType="FastqStreamer"))