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

 Type: Package

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

        (mass spectrometry data)

-Version: 2.1.10

+Version: 2.1.11

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

 Maintainer: Bernd Fischer <bernd.fischer@embl.de>, 

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

@@ -18,7 +18,7 @@ Description: mzR provides a unified API to the common file formats and

 License: Artistic-2.0

 LazyLoad: yes

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

-Imports: Biobase, zlibbioc

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

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

 VignetteBuilder: knitr

 LinkingTo: Rcpp, zlibbioc

@@ -1,6 +1,8 @@

 useDynLib(mzR)

 import(methods)

+import(BiocGenerics)

+import(ProtGenerics)

 import(zlibbioc)

 importClassesFrom(Biobase, "Versioned")

 importFrom(Biobase, validMsg)

@@ -1,5 +1,10 @@

+CHANGES IN VERSION 2.1.11

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

+ o Using generics from BiocGenerics (fileName, score) and ProtGenerics

+   [2015-02-28 Sat]

+ 

 CHANGES IN VERSION 2.1.10

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

  o Add instrumentInfo() and runInfo() for CDF backend (closes issue #22) 

  o Add precompiled libpwiz.a to reduce compile time on Windows (closes issue #21), thanks to KK

@@ -1,11 +1,7 @@

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

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

-setGeneric("psms", function(object) standardGeneric("psms"))

-setGeneric("score", function(object) standardGeneric("score"))

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

-setGeneric("modifications", function(object) standardGeneric("modifications"))

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

-setGeneric("database", function(object) standardGeneric("database"))

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

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

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

@@ -14,7 +10,6 @@ setGeneric("sampleInfo", function(object) standardGeneric("sampleInfo"))

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

 setGeneric("writeMSfile", function(object, filename, outformat) standardGeneric("writeMSfile"))

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

-setGeneric("fileName", function(object) standardGeneric("fileName"))

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

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

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

@@ -26,8 +21,18 @@ setGeneric("initializeRamp",

            signature=c("object"),

            function(object) standardGeneric("initializeRamp"))

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

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

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

 setGeneric("get3Dmap",

            signature=c("object"),

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

+

+

+### BiocGenerics

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

+## setGeneric("fileName", function(object, ...) standardGeneric("fileName"))

+

+### ProtGenerics

+## setGeneric("psms", function(object, ...) standardGeneric("psms"))

+## setGeneric("peaks", function(object, ...) standardGeneric("peaks"))

+## setGeneric("database", function(object, ...) standardGeneric("database"))

+## setGeneric("modifications", function(object, ...) standardGeneric("modifications"))

@@ -13,7 +13,7 @@ setMethod("psms",

 setMethod("score",

           signature=c("mzRident"),

-          function(object) return(object@backend$getScore()))

+          function(x) return(x@backend$getScore()))

 setMethod("para",

           signature=c("mzRident"),

@@ -23,33 +23,26 @@ setMethod("length",

           })

 setMethod("peaks",

-          signature=c("mzRnetCDF","numeric"),

-          function(object,scans) {

-

-            rawdata <- netCDFRawData(object@backend)

-

-            if (length(scans)==1) {

-              idx <- seq(rawdata$scanindex[scans]+1,

-                         min(rawdata$scanindex[scans+1],

-                             length(rawdata$mz), na.rm=TRUE))              

-              return(cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx]))

-            } else {

-              return(sapply(scans,function(x) {

-                idx <- seq(rawdata$scanindex[x]+1,

-                           min(rawdata$scanindex[x+1],

-                               length(rawdata$mz), na.rm=TRUE))

-                cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx])

-              }, simplify = FALSE))

-            }

-          })

-

-setMethod("peaks",

-          signature=c("mzRnetCDF","missing"),

-          function(object) {

-            n <- length(object)

-            if (n==1)

-              return(list(peaks(object,1:n))) ## full experiments are always returned as lists

-            return(peaks(object,1:n))

+          signature=c("mzRnetCDF"),

+          function(object, scans) {

+              if (missing(scans)) 

+                  scans <- 1:length(object)

+

+              rawdata <- netCDFRawData(object@backend)

+

+              if (length(scans) == 1) {

+                  idx <- seq(rawdata$scanindex[scans]+1,

+                             min(rawdata$scanindex[scans+1],

+                                 length(rawdata$mz), na.rm=TRUE))              

+                  return(cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx]))

+              } else {

+                  return(sapply(scans,function(x) {

+                      idx <- seq(rawdata$scanindex[x]+1,

+                                 min(rawdata$scanindex[x+1],

+                                     length(rawdata$mz), na.rm=TRUE))

+                      cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx])

+                  }, simplify = FALSE))

+              }

           })

 ## setMethod("peaksCount",

@@ -73,22 +73,18 @@ setMethod("header",

           })

 setMethod("peaks",

-          signature=c("mzRpwiz","numeric"),

-          function(object,scans) {

-            if (length(scans)==1) {

-              return(object@backend$getPeakList(scans)$peaks)

-            } else {

-              return(sapply(scans,function(x) object@backend$getPeakList(x)$peaks, simplify = FALSE))

-            }

-          })

-

-setMethod("peaks",

-          signature=c("mzRpwiz","missing"),

-          function(object) {

-            n <- length(object)

-            if (n==1)

-              return(list(peaks(object,1:n))) ## full experiments are always returned as lists

-            return(peaks(object,1:n))

+          signature=c("mzRpwiz"),

+          function(object, scans) {

+              if (mising(scans))

+                  scans <- 1:length(object)

+

+              if (length(scans) == 1) {

+                  return(object@backend$getPeakList(scans)$peaks)

+              } else {

+                  return(sapply(scans,

+                                function(x) object@backend$getPeakList(x)$peaks,

+                                simplify = FALSE))

+              }

           })

 setMethod("peaksCount",

@@ -18,22 +18,18 @@ setMethod("length",

           function(x) return(x@backend$getLastScan()))

 setMethod("peaks",

-          signature=c("mzRramp","numeric"),

-          function(object,scans) {

-            if (length(scans)==1) {

-              return(object@backend$getPeakList(scans)$peaks)

-            } else {

-              return(sapply(scans,function(x) object@backend$getPeakList(x)$peaks, simplify = FALSE))

-            }

-          })

-

-setMethod("peaks",

-          signature=c("mzRramp","missing"),

-          function(object) {

-            n <- length(object)

-            if (n==1)

-              return(list(peaks(object,1:n))) ## full experiments are always returned as lists

-            return(peaks(object,1:n))

+          signature=c("mzRramp"),

+          function(object, scans) {

+              if (missing(scans))

+                  scans <- 1:length(object)

+              

+              if (length(scans) == 1) {

+                  return(object@backend$getPeakList(scans)$peaks)

+              } else {

+                  return(sapply(scans,

+                                function(x) object@backend$getPeakList(x)$peaks,

+                                simplify = FALSE))

+              }

           })

 setMethod("peaksCount",

@@ -36,17 +36,19 @@ sampleInfo(object)

 sourceInfo(object)

 model(object)

 mzidInfo(object)

-modifications(object)

-psms(object)

+modifications(object, ...)

+psms(object, ...)

 substitutions(object)

-database(object)

+database(object, ...)

 enzymes(object)

 tolerance(object)

-score(object)

+score(x, ...)

 para(object)

 }

 \arguments{

   \item{object}{An instantiated \code{mzR} object.}

+  \item{x}{An instantiated \code{mzR} object.}

+  \item{...}{ Additional arguments, currently ignored. }

 }

 \description{

@@ -54,12 +54,12 @@

 \alias{peaksCount,mzRramp,numeric-method}

 \alias{peaksCount,mzRpwiz,missing-method}

 \alias{peaksCount,mzRpwiz,numeric-method}

-\alias{peaks,mzRramp,missing-method}

-\alias{peaks,mzRramp,numeric-method}

-\alias{peaks,mzRpwiz,missing-method}

-\alias{peaks,mzRpwiz,numeric-method}

-\alias{peaks,mzRnetCDF,missing-method}

-\alias{peaks,mzRnetCDF,numeric-method}

+\alias{peaks,mzRramp-method}

+\alias{peaks,mzRramp-method}

+\alias{peaks,mzRpwiz-method}

+\alias{peaks,mzRpwiz-method}

+\alias{peaks,mzRnetCDF-method}

+\alias{peaks,mzRnetCDF-method}

 \alias{runInfo,mzRramp-method}

 \alias{runInfo,mzRpwiz-method}

 \alias{runInfo,mzRnetCDF-method}

@@ -15,7 +15,7 @@

  isInitialized(object)

- fileName(object)

+ fileName(object, ...)

  openIDfile(filename, verbose = FALSE)

 }

@@ -26,6 +26,7 @@

     use. Currently 'Ramp', 'netCDF'  and 'pwiz' are available.}

   \item{object}{ An instantiated mzR object. }

   \item{verbose}{ Enable verbose output. }

+  \item{...}{ Additional arguments, currently ignored. }

 }

 \description{

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

  peaksCount(object, scans, ...)

- peaks(object, scans, ...)

+ peaks(object, ...)

  get3Dmap(object, scans, lowMz, highMz, resMz, ...)

 }

@@ -26,7 +26,8 @@

     peaks is returned. } 

   \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be returned.}

   \item{resMz}{a \code{numeric} defining the m/z resolution.}

-  \item{...}{Other arguments. Currently ignored.}

+  \item{...}{Other arguments. A \code{scan} parameter can be passed to

+    \code{peaks}.}

 }

 \description{