@@ -1,7 +1,7 @@

 Package: ShortRead

 Type: Package

 Title: Classes and methods for high-throughput short-read sequencing data.

-Version: 1.7.26

+Version: 1.7.27

 Author: Martin Morgan, Michael Lawrence, Simon Anders

 Maintainer: Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>

 Description: Base classes, functions, and methods for representation of

@@ -23,7 +23,7 @@ importFrom(GenomicRanges, strand)

 importFrom(Biostrings, BString, BStringSet, DNAString, DNAStringSet,

            compact, alphabetFrequency, alphabet, DNA_ALPHABET,

            quality, pairwiseAlignment, pattern,

-           trimLRPatterns, unaligned)

+           trimLRPatterns, unaligned, detail)

 importFrom(hwriter, hwrite, hwriteImage)

@@ -125,10 +125,6 @@ setGeneric("clean", function(object, ...) standardGeneric("clean"))

 setGeneric("srdistance", function(pattern, subject, ...)

            standardGeneric("srdistance"), signature=c("pattern", "subject"))

-detail <- function(object, ...) show(object)

-

-setGeneric("detail")

-

 setGeneric("alphabetScore",

            function(object, ...) standardGeneric("alphabetScore"))

@@ -14,7 +14,7 @@ setMethod(show,

           })

 setMethod(detail,

-          signature=signature(object=".ShortReadBase"),

-          function(object, ...) {

-              cat("class: ", class(object), "\n", sep="")

+          signature=signature(x=".ShortReadBase"),

+          function(x, ...) {

+              cat("class: ", class(x), "\n", sep="")

           })

@@ -294,15 +294,15 @@ setMethod(show, "AlignedRead", function(object) {

         selectSome(varLabels(alignData(object))), "\n")

 })

-setMethod(detail, "AlignedRead", function(object, ...) {

+setMethod(detail, "AlignedRead", function(x, ...) {

     callNextMethod()

-    cat("\nchromosome:", selectSome(chromosome(object)), "\n")

-    cat("position:", selectSome(position(object)), "\n")

-    cat("strand:", selectSome(strand(object)), "\n")

+    cat("\nchromosome:", selectSome(chromosome(x)), "\n")

+    cat("position:", selectSome(position(x)), "\n")

+    cat("strand:", selectSome(strand(x)), "\n")

     cat("alignQuality:\n")

-    detail(alignQuality(object))

+    detail(alignQuality(x))

     cat("\nalignData:\n")

-    show(alignData(object))

+    show(alignData(x))

 })

 ## summary

@@ -65,7 +65,7 @@ setMethod(show, "ExperimentPath", function(object) {

     for (slt in slts[slts!="basePath"]) catPath(slt)

 }

-setMethod(detail, "ExperimentPath", function(object, ...) {

+setMethod(detail, "ExperimentPath", function(x, ...) {

     callNextMethod()

-    cat("experimentPath:\n  ", experimentPath(object), "\n", sep="")

+    cat("experimentPath:\n  ", experimentPath(x), "\n", sep="")

 })

@@ -31,10 +31,10 @@ setMethod(append, c("QualityScore", "QualityScore", "missing"),

     initialize(x, quality=append(quality(x), quality(values)))

 })

-setMethod(detail, "QualityScore", function(object) {

+setMethod(detail, "QualityScore", function(x) {

     callNextMethod()

     cat("quality:\n")

-    print(quality(object))

+    print(quality(x))

 })

 ## NumericQuality

@@ -89,7 +89,7 @@ setMethod(show, "RochePath", function(object) {

     .show_additionalPathSlots(object)

 })

-setMethod(detail, "RochePath", function(object, ...) {

+setMethod(detail, "RochePath", function(x, ...) {

     callNextMethod()

-    .detail_additionalPathSlots(object)

+    .detail_additionalPathSlots(x)

 })

@@ -42,7 +42,7 @@ setMethod(lapply, "SRList", function(X, FUN, ...) {

 setMethod(show, "SRList", .SRList_show_class)

-setMethod(detail, "SRList", function(object,...) {

-    .SRList_show_class(object)

-    .srlist(object)

+setMethod(detail, "SRList", function(x,...) {

+    .SRList_show_class(x)

+    .srlist(x)

 })

@@ -58,12 +58,12 @@ setMethod(show, "SRSet", function(object) {

         sep="")

 })

-setMethod(detail, "SRSet", function(object, ...) {

+setMethod(detail, "SRSet", function(x, ...) {

     callNextMethod()

     cat("\nsourcePath\n")

-    detail(sourcePath(object), ...)

+    detail(sourcePath(x), ...)

     cat("\nphenoData\n")

-    pd <- phenoData(object)

+    pd <- phenoData(x)

     cat("pData:\n")

     print(pData(pd))

     cat("varMetadata:\n")

@@ -32,7 +32,7 @@ setMethod(show, "SRVector", function(object) {

     cat("vclass: ", vclass(object), "\n", sep="")

 })

-setMethod(detail, "SRVector", function(object) {

-    .SRList_show_class(object)

-    show(unlist(.srlist(object)))

+setMethod(detail, "SRVector", function(x) {

+    .SRList_show_class(x)

+    show(unlist(.srlist(x)))

 })

@@ -167,12 +167,12 @@ setMethod(show, "ShortRead", function(object) {

     cat("length:", length(object), "reads; width:", wd, "cycles\n")

 })

-setMethod(detail, "ShortRead", function(object, ...) {

-    cat("class: ", class(object), "\n")

+setMethod(detail, "ShortRead", function(x, ...) {

+    cat("class: ", class(x), "\n")

     cat("\nsread:\n")

-    show(sread(object))

+    show(sread(x))

     cat("\nid:\n")

-    show(id(object))

+    show(id(x))

 })

 ## summary

@@ -213,9 +213,9 @@ setMethod(alphabetScore, "ShortReadQ", .forward_objq)

 ## show

-setMethod(detail, "ShortReadQ", function(object, ...) {

+setMethod(detail, "ShortReadQ", function(x, ...) {

     callNextMethod()

-    detail(quality(object))

+    detail(quality(x))

 })

 ## summary

@@ -120,7 +120,7 @@ setMethod(show, "SolexaPath", function(object) {

     .show_additionalPathSlots(object)

 })

-setMethod(detail, "SolexaPath", function(object, ...) {

+setMethod(detail, "SolexaPath", function(x, ...) {

     callNextMethod()

-    .detail_additionalPathSlots(object)

+    .detail_additionalPathSlots(x)

 })

@@ -81,12 +81,12 @@ setMethod(show, "SolexaSet", function(object) {

     print(laneDescription(object))

 })

-setMethod(detail, "SolexaSet", function(object, ...) {

+setMethod(detail, "SolexaSet", function(x, ...) {

     callNextMethod()

     cat("\n")

-    detail(solexaPath(object), ...)

+    detail(solexaPath(x), ...)

     cat("\nclass: AnnotatedDataFrame\n")

-    ld <- laneDescription(object)

+    ld <- laneDescription(x)

     cat("pData:\n")

     print(pData(ld))

     cat("varMetadata:\n")

@@ -197,7 +197,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, by class "ShortReadQ", distance 3.

     \item{show}{\code{signature(object = "AlignedRead")}: provide a

       compact display of the \code{AlignedRead}  content.}

-    \item{detail}{\code{signature(object = "AlignedRead")}: display

+    \item{detail}{\code{signature(x = "AlignedRead")}: display

       \code{alignData} in more detail.}

   }

 }

@@ -218,5 +218,9 @@ ltrim0 <- function(x) {

     Rle(runValue(x)[i], runLength(x)[i])

 }

 endoapply(cvg, ltrim0)

+## demonstration of show() and detail() methods

+show(aln)

+detail(aln)

 }

+

 \keyword{classes}

@@ -51,8 +51,8 @@

     \item{show}{\code{signature(object = "ExperimentPath")}: briefly

       summarize the file paths of \code{object}.}

-    \item{detail}{\code{signature(object = "ExperimentPath")}: summarize

-      file paths of \code{object}.}

+    \item{detail}{\code{signature(x = "ExperimentPath")}: summarize

+      file paths of \code{x}.}

   }

 }

@@ -160,7 +160,7 @@

     }

-    \item{detail}{\code{signature(object = "QualityScore")}:

+    \item{detail}{\code{signature(x = "QualityScore")}:

       provide a more detailed view of object content.

@@ -138,7 +138,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, by class ".Roche", distance 2.

     \item{show}{\code{signature(object = "RochePath")}: Briefly

       summarize the experiment path locations.}

-    \item{detail}{\code{signature(object = "RochePath")}: Provide

+    \item{detail}{\code{signature(x = "RochePath")}: Provide

       additional detail on the Roche path. All file paths are presented

       in full.}

   }

@@ -73,7 +73,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, directly.

     \item{show}{\code{signature(object = "SRSet")}: display the contents

       of this object.}

-    \item{detail}{\code{signature(object = "SRSet")}: provide more

+    \item{detail}{\code{signature(x = "SRSet")}: provide more

       extensive information on the object.}

   }

 }

@@ -181,7 +181,7 @@

       informative summary of the object content, including the length of

       the list represented by \code{object}.}

-    \item{detail}{\code{signature(object = "SRList")}: display a more

+    \item{detail}{\code{signature(x = "SRList")}: display a more

       extensive version of the object, as one might expect from printing

       a standard list in R.}

@@ -196,7 +196,7 @@

       informative summary of the object content, e.g., the vector class

       (\code{vclass}) and length.}

-    \item{detail}{\code{signature(object = "SRVector")}: display a more

+    \item{detail}{\code{signature(x = "SRVector")}: display a more

       extensive version of the object, as one might expect from a

       printing a standard R list.}

@@ -158,7 +158,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, directly.

     \item{show}{\code{signature(object = "ShortRead")}: provides a brief

       summary of the object, including its class, length and width.}

-    \item{detail}{\code{signature(object = "ShortRead")}: provides a

+    \item{detail}{\code{signature(x = "ShortRead")}: provides a

       more extensive summary of this object, displaying the first and

       last entries of \code{sread} and \code{id}.}

@@ -146,7 +146,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, by class "ShortRead", distance 2.

 	  \code{lane} to identify the object and returning an instance of

 	  \code{\linkS4class{ShortReadQQA}}. See \code{\link{qa}}}

-    \item{detail}{\code{signature(object = "ShortReadQ")}: display the

+    \item{detail}{\code{signature(x = "ShortReadQ")}: display the

 	  first and last entries of each of \code{sread}, \code{id}, and

 	  \code{quality} entries of \code{object}.}

   }

@@ -189,8 +189,8 @@ Class \code{"\linkS4class{.ShortReadBase}"}, by class ".Solexa", distance 2.

       \code{experimentPath} is given in full; the remaining paths are

       identified by their leading characters.}

-    \item{detail}{\code{signature(object = "SolexaPath")}: summarize

-      file paths of \code{object}. All file paths are presented in

+    \item{detail}{\code{signature(x = "SolexaPath")}: summarize

+      file paths of \code{x}. All file paths are presented in

       full.}

   }

 }

@@ -69,7 +69,7 @@ Class \code{"\linkS4class{.ShortReadBase}"}, by class ".Solexa", distance 2.

       summarize the experiment path and lane description of the Solexa

       set. }

-    \item{detail}{\code{signature(object = "SolexaSet")}: Provide

+    \item{detail}{\code{signature(x = "SolexaSet")}: Provide

       additional detail on the Solexa set, including the content of

       \code{solexaPath} and the \code{pData} and \code{varMetadata} of

       \code{laneDescription}.}

deleted file mode 100644

@@ -1,42 +0,0 @@

-\name{detail}

-

-\alias{detail}

-

-\title{Show (display) detailed object content}

-

-\description{

-

-  This is a variant of \code{\link{show}}, offering a more detailed

-  display of object content.

-

-}

-\usage{

-

-detail(object, ...)

-

-}

-

-\arguments{

-

-  \item{object}{An object derived from class \code{ShortRead}. See help

-    pages for individual objects, e.g.,

-    \code{\linkS4class{ShortReadQ}}. The default simply invokes

-    \code{\link{show}}.}

-

-  \item{...}{Additional arguments. The default definition makes no use

-    of these arguments.}

-

-}

-\value{

-

-  None; the function is invoked for its side effect (detailed display of

-  object content).

-

-}

-\author{Martin Morgan}

-\examples{

-sp <- SolexaPath(system.file('extdata', package='ShortRead'))

-show(sp)

-detail(sp)

-}

-\keyword{manip}