@@ -15,4 +15,4 @@ apt_packages:

 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,

 # Thanks to jimhester pointing this out!

 before_install:

-  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi

+  - echo "$TRAVIS_R_VERSION_STRING" ; if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'SHLIB_CXX1XLD=g++ \nCXX1X=g++ ' > ~/.R/Makevars; fi

\ No newline at end of file

@@ -25,7 +25,7 @@ exportMethods(close,

               detector,

               header,

               peaksCount,

-              peaks,

+              peaks, spectra,

               get3Dmap,

               softwareInfo,

               sampleInfo,

@@ -1,14 +1,19 @@

 CHANGES IN VERSION 2.9.1

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

+ o Delete RAMPAdapter pointer in pwiz backend (by jotsetung)

+   <2016-11-20 Sun>

+ o Use spectra in addition to peaks (see issue #15)

+   <2016-12-09 Fri>

+ o New pwiz (commit 946d23d75dc70a7a4913d8e05e3d59b9255f278e)

 CHANGES IN VERSION 2.9.0

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

- o Version for Bioc devel 3.5

+ o Bioc devel 3.5

 CHANGES IN VERSION 2.8.0

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

- o Version for Bioc release 3.4

- 

+ o Bioc release 3.4

+

 CHANGES IN VERSION 2.7.13

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

  o Fix waring on OSX (see issue #60)

@@ -22,29 +22,32 @@ setMethod("length",

             return(length(scanindex))

           })

-setMethod("peaks",

-          signature=c("mzRnetCDF"),

+setMethod("peaks", "mzRnetCDF",

           function(object, scans) {

-              if (missing(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]))

+                  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])

+                  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("spectra", "mzRnetCDF",

+          function(object, scans) peaks(object, scans))

+

 ## setMethod("peaksCount",

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

 ##           function(object,scans) {

@@ -59,38 +59,28 @@ setMethod("detector",

           })

 setMethod("header",

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

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

           function(object) return(object@backend$getAllScanHeaderInfo()))

 setMethod("header",

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

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

           function(object, scans) {

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

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

               return(object@backend$getScanHeaderInfo(scans))

             } else {

               return(data.frame(t(sapply(scans,function(x) unlist(object@backend$getScanHeaderInfo(x))))))

             }

           })

-setMethod("peaks",

-          signature=c("mzRpwiz"),

-          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("peaks", "mzRpwiz",

+          function(object, scans) .peaks(object, scans))

+setMethod("spectra", "mzRpwiz",

+          function(object, scans) .peaks(object, scans))

 setMethod("peaksCount",

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

-          function(object,scans) {

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

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

+          function(object, scans) {

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

               return(object@backend$getPeakList(scans)$peaksCount)

             } else {

               return(sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount))

@@ -98,14 +88,14 @@ setMethod("peaksCount",

           })

 setMethod("peaksCount",

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

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

           function(object) {

             n <- length(object)

             return(peaksCount(object,1:n))

           })

 setMethod("runInfo",

-          signature="mzRpwiz",

+          signature = "mzRpwiz",

           function(object) {

             hd <- header(object)

             ll <- list()

@@ -7,7 +7,7 @@ setMethod("initializeRamp",

           signature="mzRramp",

           function(object) {

             if (!file.exists(fileName(object)))

-              stop("File ",fileName(object)," not found.\n")

+                stop("File ", fileName(object), " not found.\n")

             object@backend$open(fileName(object), declaredOnly = TRUE)

             if (isInitialized(object)) invisible(TRUE)

             else stop("Could not initialize ramp slot.")

@@ -17,36 +17,27 @@ setMethod("length",

           signature=c("mzRramp"),

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

-setMethod("peaks",

-          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("peaks", "mzRramp",

+          function(object, scans) .peaks(object, scans))

+

+setMethod("spectra", "mzRramp",

+          function(object, scans) .peaks(object, scans))

 setMethod("peaksCount",

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

           function(object,scans) {

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

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

-            } else {

-              return(sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount))

-            }

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

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

+              } else {

+                  return(sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount))

+              }

           })

 setMethod("peaksCount",

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

           function(object) {

-            n <- length(object)

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

+              n <- length(object)

+              return(peaksCount(object,1:n))

           })

 setMethod("header",

@@ -56,11 +47,11 @@ setMethod("header",

 setMethod("header",

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

           function(object, scans) {

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

-              return(object@backend$getScanHeaderInfo(scans))

-            } else {

-              return(data.frame(t(sapply(scans,function(x) unlist(object@backend$getScanHeaderInfo(x))))))

-            }

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

+                  return(object@backend$getScanHeaderInfo(scans))

+              } else {

+                  return(data.frame(t(sapply(scans,function(x) unlist(object@backend$getScanHeaderInfo(x))))))

+              }

           })

 setMethod("close", 

@@ -74,87 +65,87 @@ setMethod("isInitialized",

 setMethod("runInfo",

           signature="mzRramp",

           function(object) {

-            ##return(object@backend$getRunInfo())

-            hd <- header(object)

-            ll <- list()

-            ll$'scanCount' <- length(object)

-            ll$'lowMz' <- min(hd$lowMZ)

-            ll$'highMz' <- max(hd$highMZ)

-            ll$'dStartTime' <- min(hd$retentionTime)

-            ll$'dEndTime' <- max(hd$retentionTime)

-            ll$'msLevels' <- unique(hd$msLevel)

-            return(ll)

+              ##return(object@backend$getRunInfo())

+              hd <- header(object)

+              ll <- list()

+              ll$'scanCount' <- length(object)

+              ll$'lowMz' <- min(hd$lowMZ)

+              ll$'highMz' <- max(hd$highMZ)

+              ll$'dStartTime' <- min(hd$retentionTime)

+              ll$'dEndTime' <- max(hd$retentionTime)

+              ll$'msLevels' <- unique(hd$msLevel)

+              return(ll)

           })

 setMethod("instrumentInfo",

           signature="mzRramp",

           function(object) 

-          return(object@backend$getInstrumentInfo()))

+              return(object@backend$getInstrumentInfo()))

 setMethod("manufacturer",

           signature="mzRramp",

           function(object) {

-            info <- instrumentInfo(object)           

-            return(info$manufacturer)

+              info <- instrumentInfo(object)           

+              return(info$manufacturer)

           })

 setMethod("model",

           signature="mzRramp",

           function(object) {

-            info <- instrumentInfo(object)           

-            return(info$model)

+              info <- instrumentInfo(object)           

+              return(info$model)

           })

 setMethod("ionisation",

           signature="mzRramp",

           function(object) {

-            info <- instrumentInfo(object)           

-            return(info$ionisation)

+              info <- instrumentInfo(object)           

+              return(info$ionisation)

           })

 setMethod("analyzer",

           signature="mzRramp",

           function(object) {

-            info <- instrumentInfo(object)           

-            return(info$analyzer)

+              info <- instrumentInfo(object)           

+              return(info$analyzer)

           })

 setMethod("detector",

           signature="mzRramp",

           function(object) {

-            info <- instrumentInfo(object)           

-            return(info$detector)

+              info <- instrumentInfo(object)           

+              return(info$detector)

           })

 setMethod("show",

           signature="mzRramp",

           function(object) {

-            if (!isInitialized(object)) {

-              cat("Your object's ramp slot is not initialized.\n")

-              cat("Use initializeRamp(object) to fix this.\n")

-            } else {

-              filename <- fileName(object)

-              ## info <- instrumentInfo(object)

-              ## run  <- runInfo(object)

-              cat("Mass Spectrometry file handle.\n")

-              cat("Filename: ", basename(filename), "\n")

-              cat("Number of scans: ", length(object), "\n")

-              ## if (any(info != "")) {

-              ##   cat("Manufacturer: ", info$manufacturer, "\n")

-              ##   cat("Model:        ", info$model, "\n")

-              ##   cat("Ionisation:   ", info$ionisation, "\n")

-              ##   cat("Analyzer:     ", info$analyzer, "\n")

-              ##   cat("Detector:     ", info$detector, "\n")

-              ## }

-              ## cat("Number of scans: ", run$scanCount, "\n")

-              ## cat("lowMZ:        ", run$lowMZ, " \thighMZ: ", run$highMZ, "\n")

-              ## cat("startMZ:      ", run$startMZ, " \tendMZ: ",  run$endMZ, "\n")

-              ## cat("dStartTime:   ", run$dStartTime, " \tdEndTime: ", run$dEndTime, "\n")

-            }

-            invisible(NULL)

+              if (!isInitialized(object)) {

+                  cat("Your object's ramp slot is not initialized.\n")

+                  cat("Use initializeRamp(object) to fix this.\n")

+              } else {

+                  filename <- fileName(object)

+                  ## info <- instrumentInfo(object)

+                  ## run  <- runInfo(object)

+                  cat("Mass Spectrometry file handle.\n")

+                  cat("Filename: ", basename(filename), "\n")

+                  cat("Number of scans: ", length(object), "\n")

+                  ## if (any(info != "")) {

+                  ##   cat("Manufacturer: ", info$manufacturer, "\n")

+                  ##   cat("Model:        ", info$model, "\n")

+                  ##   cat("Ionisation:   ", info$ionisation, "\n")

+                  ##   cat("Analyzer:     ", info$analyzer, "\n")

+                  ##   cat("Detector:     ", info$detector, "\n")

+                  ## }

+                  ## cat("Number of scans: ", run$scanCount, "\n")

+                  ## cat("lowMZ:        ", run$lowMZ, " \thighMZ: ", run$highMZ, "\n")

+                  ## cat("startMZ:      ", run$startMZ, " \tendMZ: ",  run$endMZ, "\n")

+                  ## cat("dStartTime:   ", run$dStartTime, " \tdEndTime: ", run$dEndTime, "\n")

+              }

+              invisible(NULL)

           })

 setMethod("isolationWindow", "mzRramp",

@@ -1,3 +1,16 @@

+.peaks <- 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("isolationWindow", "character",

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

deleted file mode 100644

@@ -77,11 +77,19 @@ test_mzData.gz <- function() {

     close(mzdata)    

 }

+<<<<<<< HEAD

 test_peaks_scans <- function() {

+=======

+test_peaks_spectra <- function() {

+>>>>>>> master

     library("msdata")

     f <- proteomics(full.names = TRUE)

     x <- openMSfile(f[1])

     p <- peaks(x, 1:10)

+<<<<<<< HEAD

     s <- scans(x, 1:10)

+=======

+    s <- spectra(x, 1:10)

+>>>>>>> master

     checkIdentical(p, s)

 }

@@ -55,11 +55,11 @@

 \alias{peaksCount,mzRpwiz,missing-method}

 \alias{peaksCount,mzRpwiz,numeric-method}

 \alias{peaks,mzRramp-method}

-\alias{peaks,mzRramp-method}

-\alias{peaks,mzRpwiz-method}

+\alias{spectra,mzRramp-method}

 \alias{peaks,mzRpwiz-method}

+\alias{spectra,mzRpwiz-method}

 \alias{peaks,mzRnetCDF-method}

-\alias{peaks,mzRnetCDF-method}

+\alias{spectra,mzRnetCDF-method}

 \alias{runInfo,mzRramp-method}

 \alias{runInfo,mzRpwiz-method}

 \alias{runInfo,mzRnetCDF-method}

@@ -152,6 +152,10 @@

     \item{peaks}{\code{signature(object = "mzRramp", scans = "numeric")}: ... }

     \item{peaks}{\code{signature(object = "mzRnetCDF", scans = "missing")}: ... }

     \item{peaks}{\code{signature(object = "mzRnetCDF", scans = "numeric")}: ... }

+    \item{spectra}{\code{signature(object = "mzRramp", scans = "missing")}: ... }

+    \item{spectra}{\code{signature(object = "mzRramp", scans = "numeric")}: ... }

+    \item{spectra}{\code{signature(object = "mzRnetCDF", scans = "missing")}: ... }

+    \item{spectra}{\code{signature(object = "mzRnetCDF", scans = "numeric")}: ... }

     \item{runInfo}{\code{signature(object = "mzRramp")}: ... }

   }

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

 \name{peaks}

 \alias{peaks}

+\alias{spectra}

 \alias{header}

 \alias{peaksCount}

 \alias{get3Dmap}

@@ -13,7 +14,9 @@

  peaksCount(object, scans, ...)

- peaks(object, ...)

+ peaks(object, ...) 

+

+ spectra(object, ...) ## same as peaks

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

 }

@@ -21,7 +24,7 @@

 \arguments{

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

   \item{scans}{A \code{numeric} specifying which scans to

-    return. Optional for the \code{header}, \code{peaks} and

+    return. Optional for the \code{header}, \code{peaks}, \code{scans} and

     \code{peaksCount} methods. If ommited, the requested data for all

     peaks is returned. } 

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

@@ -31,25 +34,27 @@

 }

 \description{

-  Access the MS raw data. The \code{peaks} and \code{peaksCount}

-  functions return the (m/z,intensity) pairs and the number peaks in the

-  spectrum/spectra. \code{peaks} returns a single matrix if \code{scans}

-  is a \code{numeric} of length 1 and a list of matrices if several scans are

-  asked for or no \code{scans} argument is provided (i.e all spectra in

-  the oject are retured). \code{peaksCount} will return a numeric of

-  length \code{n}. 

+

+  Access the MS raw data. The \code{peaks}, \code{spectra} (can be used

+  interchangeably) and \code{peaksCount} functions return the (m/z,

+  intensity) pairs and the number peaks in the

+  spectrum/spectra. \code{peaks} and \code{spectra} return a single matrix

+  if \code{scans} is a \code{numeric} of length 1 and a list of matrices

+  if several scans are asked for or no \code{scans} argument is provided

+  (i.e all spectra in the oject are retured). \code{peaksCount} will

+  return a numeric of length \code{n}.

   The \code{\link{header}} function returns a list containing

- \code{seqNum}, \code{acquisitionNum} , \code{msLevel},

- \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},

- \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},

- \code{ionisationEnergy}, \code{lowM}, \code{highMZ},

- \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},

- \code{precursorIntensity}, \code{mergedScan},

- \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and 

- \code{mergedResultEndScanNum}, when available in the original file. If

- multiple scans are queried, a \code{data.frame} is returned with the

- scans reported along the rows.

+  \code{seqNum}, \code{acquisitionNum} , \code{msLevel},

+  \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},

+  \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},

+  \code{ionisationEnergy}, \code{lowM}, \code{highMZ},

+  \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},

+  \code{precursorIntensity}, \code{mergedScan},

+  \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and

+  \code{mergedResultEndScanNum}, when available in the original file. If

+  multiple scans are queried, a \code{data.frame} is returned with the

+  scans reported along the rows.

  The \code{get3Dmap} function performs a simple resampling between

  \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix of

@@ -66,7 +71,6 @@

   Steffen Neumann and Laurent Gatto

 }

-

 \examples{

  library(msdata)

  filepath <- system.file("microtofq", package = "msdata")