@@ -2,7 +2,7 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.7.5

+Version: 2.7.6

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,

 	    Steffen Neumann <sneumann@ipb-halle.de>,

@@ -19,7 +19,7 @@ License: Artistic-2.0

 LazyLoad: yes

 Depends: Rcpp (>= 0.10.1), methods, utils

 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics

-Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr

+Suggests: msdata (>= 0.3.5), RUnit, mzID, BiocStyle, knitr, XML

 VignetteBuilder: knitr

 LinkingTo: Rcpp, zlibbioc

 RcppModules: Ramp, Pwiz, Ident

@@ -19,6 +19,7 @@ exportMethods(close,

               chromatogramsInfo,

               manufacturer,

               model,

+	      isolationWindow,

               ionisation,

               analyzer,

               detector,

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 2.7.6

+------------------------

+ o new isolationWindow accessor <2016-09-23 Fri>

+ 

 CHANGES IN VERSION 2.7.5

 ------------------------

  o Apply Martin's free/delete patch - see

@@ -18,14 +18,17 @@ setGeneric("analyzer", function(object) standardGeneric("analyzer"))

 setGeneric("detector", function(object) standardGeneric("detector"))

 setGeneric("isInitialized", function(object) standardGeneric("isInitialized"))

 setGeneric("initializeRamp",

-           signature=c("object"),

+           signature = c("object"),

            function(object) standardGeneric("initializeRamp"))

-setGeneric("header", function(object,scans,...) standardGeneric("header"))

-setGeneric("peaksCount", function(object,scans,...) standardGeneric("peaksCount"))

+setGeneric("header", function(object, scans, ...) standardGeneric("header"))

+setGeneric("peaksCount",

+           function(object, scans, ...) standardGeneric("peaksCount"))

 setGeneric("get3Dmap",

-           signature=c("object"),

-           function(object,scans,lowMz,highMz,resMz,...) standardGeneric("get3Dmap"))

-

+           signature = c("object"),

+           function(object, scans, lowMz, highMz, resMz, ...)

+               standardGeneric("get3Dmap"))

+setGeneric("isolationWindow",

+           function(object, ...) standardGeneric("isolationWindow"))

 ### BiocGenerics

 ## setGeneric("score", function(x, ...) standardGeneric("score"))

@@ -161,3 +161,5 @@ pwiz.version <- function() {

     .Call('mzR_pwiz_version', PACKAGE = 'mzR')

 }

+setMethod("isolationWindow", "mzRpwiz",

+          function(object, ...) .isolationWindow(fileName(object), ...))

@@ -157,3 +157,5 @@ setMethod("show",

             invisible(NULL)

           })

+setMethod("isolationWindow", "mzRramp",

+          function(object, ...) .isolationWindow(fileName(object), ...))

new file mode 100644

@@ -0,0 +1,29 @@

+setMethod("isolationWindow", "character",

+          function(object, ...) .isolationWindow(object, ...))

+

+

+.isolationWindow <- function(x, unique. = TRUE, simplify = TRUE) {

+    stopifnot(all(file.exists(x)))

+    if (!requireNamespace("XML"))

+        stop("Please install the XML package to use this functionality.")

+    res <- lapply(x, function(xx) {

+        xml <- XML::xmlParse(xx)

+        ns <- c(x = "http://psi.hupo.org/ms/mzml")

+        path <- c(low = "//x:isolationWindow/x:cvParam[@accession='MS:1000828']/@value",

+                  high = "//x:isolationWindow/x:cvParam[@accession='MS:1000829']/@value")

+        low <- as.numeric(XML::xpathSApply(xml, path["low"], namespaces = ns))

+        high <- as.numeric(XML::xpathSApply(xml, path["high"], namespaces = ns))

+        cbind(low, high)

+    })

+    if (.multipleIsolationWindows(res))

+        message("Found multiple isolation windows in an acquisition.")

+    if (unique.)

+        res <- lapply(res, base::unique)

+    if (simplify & length(x) == 1) res <- res[[1]]

+    return(res)

+}

+

+.multipleIsolationWindows <- function(x) {

+    x <- lapply(x, base::unique)

+    any(sapply(x, function(xx) nrow(xx) > 1))

+}

new file mode 100644

@@ -0,0 +1,21 @@

+test_isolationWindow <- function() {

+    library("msdata")

+    f <- msdata::proteomics(full.names = TRUE)

+    rw1 <- openMSfile(f, backend = "Ramp")

+    rw2 <- openMSfile(f, backend = "pwiz")

+    i1 <- isolationWindow(f)

+    i2 <- isolationWindow(rw1)

+    i3 <- isolationWindow(rw2)

+    checkEquals(i1, i2)

+    checkEquals(i1, i3)

+    i1 <- isolationWindow(f, unique = FALSE)

+    i2 <- isolationWindow(rw1, unique = FALSE)

+    i3 <- isolationWindow(rw2, unique = FALSE)

+    checkEquals(i1, i2)

+    checkEquals(i1, i3)

+    i1 <- isolationWindow(c(f, f), unique = FALSE)

+    checkEquals(length(i1), 2L)

+    checkEquals(i1[[1]], i1[[2]])

+    hd <- header(rw1)

+    checkEquals(sum(hd$msLevel == 2), nrow(i1[[1]]))

+}

new file mode 100644

@@ -0,0 +1,62 @@

+\name{isolationWindow-methods}

+\docType{methods}

+\alias{isolationWindow}

+\alias{isolationWindow-methods}

+\alias{isolationWindow,character-method}

+\alias{isolationWindow,mzRpwiz-method}

+\alias{isolationWindow,mzRramp-method}

+

+\title{ Returns the ion selection isolation window }

+

+\description{

+

+  The methods return matrices of lower (column \code{low}) and upper

+  (column \code{high}) isolation window offsets. Matrices are returned

+  as a list of length equal to the number of input files (provided as

+  file names of raw mass spectrometry data objects, see below). By

+  default (i.e when \code{unique. = TRUE} ), only unique offsets are

+  returned, as they are expected to identical for all spectra per

+  acquisition. If this is not the case, a message is displayed.

+  

+}

+

+

+\section{Methods}{

+  \describe{

+

+    \item{\code{signature(object = "character", unique. = "logical",

+	simplify = "logical")}}{Returns the isolation window for the

+      file \code{object}. By default, only unique isolation windows

+      are returned per file (\code{unique = TRUE}); if set to

+      \code{FALSE}, a \code{matrix} with as many rows as there are MS2

+      spectra. If only one file passed an input and \code{simplify} is

+      set to \code{TRUE} (default), the resulting \code{list} of

+      length 1 is simplified to a \code{matrix}.  }

+

+    \item{\code{signature(object = "mzRpwiz", unique. = "logical",

+	simplify = "logical")}}{As above for \code{mzRpwiz} objects. }

+

+    \item{\code{signature(object = "mzRramp", unique. = "logical",

+	simplify = "logical")}}{As above for \code{mzRramp} object. }

+

+  }

+}

+

+\author{

+

+  Laurent Gatto <lg390@cam.ac.uk> based on the functionality from the

+  \code{msPurity:::get_isolation_offsets} function.

+

+}

+

+\examples{

+library("msdata")

+f <- msdata::proteomics(full.names = TRUE)

+isolationWindow(f)

+

+rw <- openMSfile(f)

+isolationWindow(rw)

+str(isolationWindow(rw, unique = FALSE))

+}

+

+\keyword{methods}

\ No newline at end of file