@@ -1,8 +1,8 @@

 Package: ShortRead

 Type: Package

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

-Version: 0.1.51

-Author: Martin Morgan

+Version: 0.1.52

+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

 	high-throughput, short-read sequencing data.

@@ -149,16 +149,14 @@ setClass("AlignedRead", contains="ShortReadQ",

 setClass(".Solexa", contains=".ShortReadBase",

          representation=representation("VIRTUAL"))

-setClass("SolexaPath", contains=".Solexa",

+setClass("SolexaPath", contains=c("ExperimentPath", ".Solexa"),

          representation=representation(

-           experimentPath="character",

            dataPath="character",

            scanPath="character",

            imageAnalysisPath="character",

            baseCallPath="character",

            analysisPath="character"),

          prototype=prototype(

-           experimentPath=NA_character_,

            scanPath=NA_character_,

            dataPath=NA_character_,

            imageAnalysisPath=NA_character_,

@@ -76,7 +76,9 @@ setGeneric("read454",

            standardGeneric("read454"))

 setGeneric("readBaseQuality",

-           function(dirPath, seqPattern=character(0), prbPattern=character(0), ...)

+           function(dirPath,

+                    seqPattern=character(0), prbPattern=character(0),

+                    ...)

            standardGeneric("readBaseQuality"), signature="dirPath")

 setGeneric("length")

@@ -107,14 +107,17 @@ polyn <- function(nucleotides, n)

     x

 }

-.make_getter <- function(slots, where=topenv(parent.frame())) {

+.make_getter <-

+    function(slots, where=topenv(parent.frame()), verbose=FALSE)

+{

     slots <- .nameAll(slots)

     nms <- names(slots)

     ok <- !sapply(nms, exists, where)

-    if (!all(ok))

+    if (verbose && !all(ok))

         .throw(SRError("InternalError",

                       "getter '%s' already exists",

                       paste(nms[!ok], collapse=", ")))

+    slots <- slots[ok]

     for (i in seq_along(slots)) {

         func <- eval(substitute(function(object, ...) slot(object, SLOT),

                                 list(SLOT=slots[i])))

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

 setMethod(".srValidity", "ExperimentPath", function(object) {

     msg <- NULL

-    if (length(basePath(object))!=1)

-        msg <- c(msg, "ExperimentPath 'basePath' must be character(1)")

+    if (length(experimentPath(object))!=1)

+        msg <- c(msg, "ExperimentPath 'experimentPath' must be character(1)")

     if (is.null(msg)) TRUE else msg

 })

@@ -15,19 +15,30 @@ setMethod(".srValidity", "ExperimentPath", function(object) {

 }

 .checkPath <- function(path) {

-  nm <- deparse(substitute(path))

-  if (length(path)==0) {

-    warning(nm, " not defined")

-  } else {

-    for (p in path)

-      if (!file.exists(p)) 

-        warning(nm, " '", p, "' does not exist")

-  }

+    nm <- deparse(substitute(path))

+    if (length(path)==0) {

+        warning(nm, " not defined")

+    } else {

+        for (p in path)

+            if (!file.exists(p)) 

+                warning(nm, " '", p, "' does not exist")

+    }

 }

-.make_getter(slotNames("ExperimentPath"))

+ExperimentPath <- function(experimentPath, ...) {

+    new("ExperimentPath", basePath=experimentPath, ...)

+}

-setMethod("show", "ExperimentPath", function(object) {

+experimentPath <- basePath <- function(object, ...) {

+    slot(object, "basePath")

+}

+

+basePath <- function(object, ...) {

+    .Deprecated("experimentPath")

+    experimentPath(object, ...)

+}

+

+.show_additionalPathSlots <- function(object) { # for derived classes

     catPath <- function(nm) {

         vals <- do.call(nm, list(object))

         vals <- substr(basename(vals), 1, 15)

@@ -35,20 +46,26 @@ setMethod("show", "ExperimentPath", function(object) {

                       sep="")

         cat(nm, ": ", paste(vals, collapse=", "), "\n", sep="")

     }

-    callNextMethod()

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

     slts <- slotNames(object)

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

+}

+

+setMethod("show", "ExperimentPath", function(object) {

+    callNextMethod()

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

 })

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

+.detail_additionalPathSlots <- function(object) {

     catPath <- function(nm) {

         fnms <- do.call(nm, list(object))

         cat(nm, ":\n  ", paste(fnms, collapse="\n  "), sep="")

         cat("\n")

     }

-    callNextMethod()

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

     slts <- slotNames(object)

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

+}

+

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

+    callNextMethod()

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

 })

@@ -62,3 +62,13 @@ setMethod("sampleNames", "RochePath", .sampleNames_RochePath)

 }

 setMethod("runNames", "RochePath", .runNames_RochePath)

+

+setMethod("show", "RochePath", function(object) {

+    callNextMethod()

+    .show_additionalPathSlots(object)

+})

+

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

+    callNextMethod()

+    .detail_additionalPathSlots(object)

+})

@@ -15,13 +15,13 @@ setMethod(".srValidity", "SolexaPath", function(object) {

 }

 SolexaPath <- function(experimentPath,

-                        dataPath=.solexaPath(experimentPath, "Data"),

-                        scanPath=.solexaPath(dataPath, "GoldCrest"),

-                        imageAnalysisPath=.solexaPath(dataPath, "^C"),

-                        baseCallPath=.solexaPath(imageAnalysisPath,

-                          "^Bustard"),

-                        analysisPath=.solexaPath(baseCallPath,

-                          "^GERALD"),

+                       dataPath=.solexaPath(experimentPath, "Data"),

+                       scanPath=.solexaPath(dataPath, "GoldCrest"),

+                       imageAnalysisPath=.solexaPath(dataPath, "^C"),

+                       baseCallPath=.solexaPath(imageAnalysisPath,

+                         "^Bustard"),

+                       analysisPath=.solexaPath(baseCallPath,

+                         "^GERALD"),

                        ..., verbose=FALSE) {

     checkPath <- function(path) {

         nm <- deparse(substitute(path))

@@ -41,7 +41,8 @@ SolexaPath <- function(experimentPath,

         checkPath(baseCallPath)

         checkPath(analysisPath)

     }

-    new("SolexaPath", ..., experimentPath=experimentPath,

+    new("SolexaPath", ...,

+        basePath=experimentPath,

         dataPath=dataPath, scanPath=scanPath,

         imageAnalysisPath=imageAnalysisPath, baseCallPath=baseCallPath,

         analysisPath=analysisPath)

@@ -107,27 +108,11 @@ setMethod("qa", "SolexaPath", .qa_SolexaPath)

 setMethod("report", "SolexaPath", .report_SolexaPath)

 setMethod("show", "SolexaPath", function(object) {

-    catPath <- function(nm) {

-        vals <- do.call(nm, list(object))

-        vals <- substr(basename(vals), 1, 15)

-        vals <- paste(vals, ifelse(nchar(vals)==15, "...", ""),

-                      sep="")

-        cat(nm, ": ", paste(vals, collapse=", "), "\n", sep="")

-    }

     callNextMethod()

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

-    slts <- slotNames("SolexaPath")

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

+    .show_additionalPathSlots(object)

 })

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

-    catPath <- function(nm) {

-        fnms <- do.call(nm, list(object))

-        cat(nm, ":\n  ", paste(fnms, collapse="\n  "), sep="")

-        cat("\n")

-    }

     callNextMethod()

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

-    slts <- slotNames("SolexaPath")

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

+    .detail_additionalPathSlots(object)

 })

new file mode 100644

@@ -0,0 +1,63 @@

+\name{ExperimentPath-class}

+\docType{class}

+\alias{ExperimentPath-class}

+% constructors

+\alias{ExperimentPath}

+% etc

+\alias{show,ExperimentPath-method}

+\alias{detail,ExperimentPath-method}

+

+\title{"ExperimentPath" class representing a file hierarchy of data

+  files}

+

+\description{

+

+  Short read technologies often produce a hierarchy of output files. The

+  content of the hierarchy varies. This class represents the root of the

+  file hierarchy. Specific classes (e.g.,

+  \code{\linkS4class{SolexaPath}}) represent different technologies.

+

+}

+\section{Objects from the Class}{

+

+  Objects from the class are created by calls to the constructor:

+  

+  \code{ExperimentPath(experimentPath)}

+

+  \describe{

+    \item{experimentPath}{\code{character(1)} object pointing to the

+      top-level directory of the experiment; see specific technology

+      classes for additional detail.}

+    \item{verbose=FALSE}{(optional) logical vector which, when

+      \code{TRUE} results in warnings if paths do not exist.}

+  }

+  All paths must be fully-specified.

+}

+\section{Slots}{

+  \code{ExperimentPath} has one slot, containing a fully

+  specified path to the corresponding directory (described above).

+  \describe{

+    \item{\code{basePath}}{See above.}

+  }

+  The slot is accessed with \code{basePath} or \code{experimentPath}.

+}

+\section{Extends}{

+  Class \code{"\linkS4class{.ShortReadBase}"}, directly.

+}

+\section{Methods}{

+  Methods include:

+  \describe{

+

+    \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}.}

+  }

+}

+

+\author{Michael Lawrence}

+\examples{

+showClass("ExperimentPath")

+}

+\keyword{classes}

@@ -23,6 +23,7 @@

 % FastqQuality

 \alias{width,FastqQuality-method}

 \alias{show,FastqQuality-method}

+\alias{alphabet,FastqQuality-method}

 \alias{alphabetFrequency,FastqQuality-method}

 \alias{alphabetByCycle,FastqQuality-method}

 \alias{srsort,FastqQuality-method}

@@ -109,6 +110,10 @@

   The following methods are defined on specific classes:

   \describe{

+    \item{alphabet}{\code{signature(x = "FastqQuality")}:

+      Return a character vector of valid quality characters.

+    }

+

     \item{alphabetFrequency}{\code{signature(stringSet = "FastqQuality")}:

       Apply \code{\link[Biostrings]{alphabetFrequency}} to quality

@@ -3,7 +3,13 @@

 \alias{IntegerQuality}

 \alias{MatrixQuality}

 \alias{FastqQuality}

+\alias{FastqQuality,BStringSet-method}

+\alias{FastqQuality,character-method}

+\alias{FastqQuality,missing-method}

 \alias{SFastqQuality}

+\alias{SFastqQuality,BStringSet-method}

+\alias{SFastqQuality,character-method}

+\alias{SFastqQuality,missing-method}

 \title{Construct objects indicating read or alignment quality}

 \description{

@@ -22,7 +28,10 @@ SFastqQuality(quality, ...)

 \arguments{

   \item{quality}{An object used to initialize the data

     structure. Appropriate objects are indicated in the constructors

-    above.}

+    above for Numeric, Integer, and Matrix qualities. For

+    \code{FastqQuality} and \code{SFastqQuality}, methods are defined

+    for \code{\linkS4class{BStringSet}}, \code{character}, and

+    \code{missing}.}

   \item{...}{Additional arguments, currently unused.}

 }

@@ -14,6 +14,7 @@

 \alias{alignData}

 % Solexa

 \alias{experimentPath}

+\alias{basePath}

 \alias{dataPath}

 \alias{scanPath}

 \alias{imageAnalysisPath}

@@ -47,6 +48,7 @@ alignQuality(object, ...)

 alignData(object, ...)

 ## Solexa

 experimentPath(object, ...)

+basePath(object, ...)

 dataPath(object, ...)

 scanPath(object, ...)

 imageAnalysisPath(object, ...)

@@ -1,5 +1,6 @@

 \name{qa}

 \alias{qa}

+\alias{qa,character-method}

 \title{Perform quality assessment on short reads}

@@ -17,21 +18,20 @@ qa(dirPath, ...)

 \arguments{

-  \item{dirPath}{A character vector or other object locating the data

-    for which quality assessment is to be performed. See help pages for

-    defined methods (by evaluating the example code, below) for details

-    of available methods.}

+  \item{dirPath}{A character vector or other object (e.g.,

+    \code{\link{SolexaPath}}; see \code{showMethods}, below) locating

+    the data for which quality assessment is to be performed. See help

+    pages for defined methods (by evaluating the example code, below)

+    for details of available methods.}

   \item{\dots}{Additional arguments used by methods.}

 }

 \details{

-  The following general method is defined, in addition to those for

-  specific objects:

+  The following methods are defined:

   \itemize{

     \item{

       \code{dirPath="character", pattern="character", type="SolexaExport", ...}}{

-

       Quality assessment is performed on all files in directory

       \code{dirPath} whose file name matches \code{pattern}. The type of

       analysis performed is based on the \code{type} argument.

@@ -1,5 +1,6 @@

 \name{report}

 \alias{report}

+\alias{report,character-method}

 \title{Summarize quality assessment results into a report}

@@ -29,6 +30,15 @@ report(x, ..., dest = tempfile(), type = "pdf")

     report types depend on the type of object \code{x}.}

 }

+\details{

+  The following methods are defined:

+  \itemize{

+    \item{

+      \code{dirPath="character", ..., dest=tempfile(), type="pdf"}

+    }{This method is used internally}

+  }

+}

+

 \value{

   This function is invoked for its side effect;  the return value is the

   name of the directory or file where the report was created.