Removed netCDF.h, can already be used by xcmsRaw

sneumann · Sep 10, 2018 · dfbd825 · dfbd825
1 parent bda1e08
commit dfbd825
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Showing 9 changed files with 128 additions and 370 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,12 +17,12 @@ 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, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)
+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1), ncdf4
 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML
 VignetteBuilder: knitr
 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
 RcppModules: Ramp, Pwiz, Ident
-SystemRequirements: C++11, GNU make, NetCDF
+SystemRequirements: C++11, GNU make
 URL: https://github.com/sneumann/mzR/
 BugReports: https://github.com/sneumann/mzR/issues/
 biocViews: Infrastructure, DataImport, Proteomics, Metabolomics,

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,8 +6,8 @@ import(ProtGenerics)
 importClassesFrom(Biobase, "Versioned")
 importFrom(Biobase, validMsg)
 importFrom("utils", "packageVersion")
-##importFrom(Rcpp, "loadRcppModules")
 import(Rcpp)
+import(ncdf4)
 
 export(openMSfile,
        openIDfile,

diff --git a/R/DataClasses.R b/R/DataClasses.R
@@ -2,8 +2,10 @@
 ## Defines supported backend APIs
 ##  - NULL: default
 ##  - C++Object: for Rcpp modules for ramp and pwiz backends
+##  - ncdf4 for netCDF files
+setOldClass("ncdf4")
 setClassUnion("msAPI",
-              c("C++Object","integer", "NULL"))
+              c("C++Object","ncdf4", "NULL"))
 
 ##############################################################
 ## mzR main virtual class
@@ -60,10 +62,18 @@ setClass("mzRpwiz",
 ##############################################################
 ## mzRnetCDF - netCDF backend 
 setClass("mzRnetCDF",
-         representation(),
+         representation(backend="ncdf4"),
          contains=c("mzR"),
          prototype=prototype(
-           new("Versioned", versions=c(mzR="0.0.1")))
+             new("Versioned", versions=c(mzR="0.0.2"))),
+         validity=function(object) {
+             msg <- validMsg(NULL,NULL)
+             if (is.null(object@backend))
+                 msg <- validMsg(msg,"ncdf4 object not initialised.")
+             if (is.null(object@backend$id))
+                 msg <- validMsg(msg,"ncdf4 object is closed.")
+             if (is.null(msg)) TRUE
+             else msg }
          )
 
 ##############################################################

diff --git a/R/methods-mzRnetCDF.R b/R/methods-mzRnetCDF.R
@@ -1,25 +1,7 @@
-## setMethod("get3Dmap",
-##           signature="mzRnetCDF",
-##           function(object,scans,lowMz,highMz,resMz) 
-##           return(object@backend$get3DMap(scans,lowMz,highMz,resMz)))
-
-## setMethod("initializeRamp",
-##           signature="mzRnetCDF",
-##           function(object) {
-##             if (!file.exists(fileName(object)))
-##               stop("File ",fileName(object)," not found.\n")
-##             object@backend$open(fileName(object), declaredOnly = TRUE)
-##             if (isInitialized(object)) invisible(TRUE)
-##             else stop("Could not initialize ramp slot.")
-##           })
-
 setMethod("length",
           signature=c("mzRnetCDF"),
           function(x) {
-            scanindex <- netCDFVarInt(x@backend, "scan_index")
-            if (!is.null(attr(scanindex, "errortext")))
-              stop("Couldn't read scan indicies from ", x@backend)
-            return(length(scanindex))
+              return(netCDFVarLen(x@backend, var="scan_number"))
           })
 
 setMethod("peaks", "mzRnetCDF",
@@ -102,11 +84,15 @@ setMethod("header",
 
 setMethod("close", 
           signature="mzRnetCDF",
-          function(con,...) return( netCDFClose(con@backend) ))
+          function(con,...) {
+              if (validObject(con))
+                  netCDFClose(con@backend)
+              con@backend$id <- NULL
+              invisible(TRUE)} )
 
 setMethod("isInitialized", 
           signature="mzRnetCDF",
-          function(object) return(object@backend > 0))
+          function(object) return(class(object@backend) == "ncdf4" && validObject(object)))
 
 setMethod("runInfo",
            signature="mzRnetCDF",