@@ -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,

@@ -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,

@@ -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 }

          )

 ##############################################################

@@ -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",

@@ -1,152 +1,119 @@

-netCDFStrError <- function(ncerr) {

-

-    buflen <- 255

-    

-    .C("NetCDFStrError",

-       as.integer(ncerr),

-       as.integer(buflen),

-       out = paste(rep(" ", buflen), collapse = ""),

-       PACKAGE = "mzR")$out

-}

 netCDFIsFile <- function(filename) {

-

-    ncid <- netCDFOpen(filename)

-    if (!is.null(attr(ncid, "errortext")))

-        return(FALSE)

-    netCDFClose(ncid)

-    

-    return(TRUE)

+    result <- tryCatch({

+        ncid <- nc_open(filename)

+        result <- !is.null(ncid)

+        netCDFClose(ncid)

+        return(result)

+    },

+    error=function(cond) return(FALSE)

+    )

 }

 netCDFOpen <- function(filename) {

-

-    result <- .C("NetCDFOpen",

-                 as.character(filename),

-                 ncid = integer(1),

-                 status = integer(1),

-                 PACKAGE = "mzR")

-    

-    if (result$status)

-        return(structure(result$status, 

-                         errortext = netCDFStrError(result$status)))

-    

-    return(result$ncid)

+    result <- nc_open(filename, write=FALSE) 

+    return(result)

 }

 netCDFClose <- function(ncid) {

-

-    result <- .C("NetCDFClose",

-                 as.integer(ncid),

-                 status = integer(1),

-                 PACKAGE = "mzR")

-    

-    if (result$status)

-        return(structure(result$status, 

-                         errortext = netCDFStrError(result$status)))

-

-    result$status

+    result <- tryCatch({

+##        closedncid <- nc_close(ncid)        

+        return(TRUE)

+    },

+    error=function(cond) return(FALSE)

+    )

 }

 netCDFVarID <- function(ncid, var) {

-

-    result <- .C("NetCDFVarID",

-                 as.integer(ncid),

-                 as.character(var),

-                 id = integer(1),

-                 status = integer(1),

-                 PACKAGE = "mzR")

-    

-    if (result$status)

-        return(structure(result$status, 

-                         errortext = netCDFStrError(result$status)))

-    

-    return(result$id)

+stop()

+    ## result <- .C("NetCDFVarID",

+    ##              as.integer(ncid),

+    ##              as.character(var),

+    ##              id = integer(1),

+    ##              status = integer(1),

+    ##              PACKAGE = "mzR")

+    

+    ## if (result$status)

+    ##     return(structure(result$status, 

+    ##                      errortext = netCDFStrError(result$status)))

+    

+    ## return(result$id)

 }

 netCDFVarLen <- function(ncid, var) {

-    if (is.character(var))

-        var <- netCDFVarID(ncid, var)

-    

-    result <- .C("NetCDFVarLen",

-                 as.integer(ncid),

-                 as.integer(var),

-                 len = integer(1),

-                 status = integer(1),

-                 PACKAGE = "mzR")

+    return(ncid$dim[[var]]$len)

-    if (result$status)

-        return(structure(result$status, 

-                         errortext = netCDFStrError(result$status)))

-    

-    return(result$len)

 }

 netCDFVarDouble <- function(ncid, var) {

+    as.vector(ncvar_get(ncid, varid=var))

+}

+netCDFVarInt <- function(ncid, var) {

+    as.vector(ncvar_get(ncid, varid=var))

+}

+netCDFVarText <- function(ncid, var) {

+    as.vector(ncvar_get(ncid, varid=var))

+}

+

+## netCDFVarDouble <- function(ncid, var) {

-    if (is.character(var))

-        var <- netCDFVarID(ncid, var)

+##     if (is.character(var))

+##         var <- netCDFVarID(ncid, var)

-    if (!is.null(attr(var, "errortext")))

-        return(var)

+##     if (!is.null(attr(var, "errortext")))

+##         return(var)

-    len <- netCDFVarLen(ncid, var)

-    if (!is.null(attr(len, "errortext")))

-        return(len)

+##     len <- netCDFVarLen(ncid, var)

+##     if (!is.null(attr(len, "errortext")))

+##         return(len)

-    .C("NetCDFVarDouble",

-       as.integer(ncid),

-       as.integer(var),

-       data = double(len),

-       status = integer(1),

-       PACKAGE = "mzR")$data

-}

+##     .C("NetCDFVarDouble",

+##        as.integer(ncid),

+##        as.integer(var),

+##        data = double(len),

+##        status = integer(1),

+##        PACKAGE = "mzR")$data

+## }

-netCDFVarInt <- function(ncid, var) {

+## netCDFVarInt <- function(ncid, var) {

-    if (is.character(var))

-        var <- netCDFVarID(ncid, var)

+##     if (is.character(var))

+##         var <- netCDFVarID(ncid, var)

-    if (!is.null(attr(var, "errortext")))

-        return(var)

+##     if (!is.null(attr(var, "errortext")))

+##         return(var)

-    len <- netCDFVarLen(ncid, var)

-    if (!is.null(attr(len, "errortext")))

-        return(len)

+##     len <- netCDFVarLen(ncid, var)

+##     if (!is.null(attr(len, "errortext")))

+##         return(len)

-    .C("NetCDFVarInt",

-       as.integer(ncid),

-       as.integer(var),

-       data = integer(len),

-       status = integer(1),

-       PACKAGE = "mzR")$data

-}

+##     .C("NetCDFVarInt",

+##        as.integer(ncid),

+##        as.integer(var),

+##        data = integer(len),

+##        status = integer(1),

+##        PACKAGE = "mzR")$data

+## }

-netCDFVarText <- function(ncid, var) {

+## netCDFVarText <- function(ncid, var) {

-    if (is.character(var))

-        var <- netCDFVarID(ncid, var)

+##     if (is.character(var))

+##         var <- netCDFVarID(ncid, var)

-    if (!is.null(attr(var, "errortext")))

-        return(var)

+##     if (!is.null(attr(var, "errortext")))

+##         return(var)

-    .C("NetCDFVarText",

-       as.integer(ncid),

-       as.integer(var),

-       data = character(1),

-       status = integer(1),

-       PACKAGE = "mzR")$data

-}

+##     .C("NetCDFVarText",

+##        as.integer(ncid),

+##        as.integer(var),

+##        data = character(1),

+##        status = integer(1),

+##        PACKAGE = "mzR")$data

+## }

 netCDFAttText <- function(ncid, att) {

-

-    .C("NetCDFGlobalAttribute",

-       as.integer(ncid),

-       as.character(att),

-       data = character(1),

-       status = integer(1),

-       PACKAGE = "mzR")$data

+    ncatt_get(ncid, varid=0, attname=att)$value

 }

@@ -154,42 +121,34 @@ netCDFMSPoints <- function(ncid, scanIndex) {

     if (!is.integer(scanIndex)) scanIndex <- as.integer(scanIndex)

-    var <- netCDFVarID(ncid, "mass_values")

-    if (!is.null(attr(var, "errortext")))

-        return(var)

-    

-    len <- netCDFVarLen(ncid, var)

-    if (!is.null(attr(len, "errortext")))

-        return(len)

-    

-    .C("NetCDFMSPoints",

-       as.integer(ncid),

-       as.integer(length(scanIndex)),

-       scanIndex,

-       as.integer(len),

-       massValues = double(len),

-       intensityValues = double(len),

-       status = integer(1),

-       PACKAGE = "mzR")[c("massValues", "intensityValues")]

+    return (cbind.data.frame(massValues=netCDFVarDouble(ncid, "mass_values"),

+                             intensityValues=netCDFVarDouble(ncid, "intensity_values")))

+    

+    ## var <- netCDFVarID(ncid, "mass_values")

+    ## if (!is.null(attr(var, "errortext")))

+    ##     return(var)

+    

+    ## len <- netCDFVarLen(ncid, var)

+    ## if (!is.null(attr(len, "errortext")))

+    ##     return(len)

+    

+    ## .C("NetCDFMSPoints",

+    ##    as.integer(ncid),

+    ##    as.integer(length(scanIndex)),

+    ##    scanIndex,

+    ##    as.integer(len),

+    ##    massValues = double(len),

+    ##    intensityValues = double(len),

+    ##    status = integer(1),

+    ##    PACKAGE = "mzR")[c("massValues", "intensityValues")]

 }

 netCDFRawData <- function(ncid) {

     rt <- netCDFVarDouble(ncid, "scan_acquisition_time")

-    if (!is.null(attr(rt, "errortext")))

-        stop("Couldn't read scan times")

-    

     tic <- netCDFVarDouble(ncid, "total_intensity")

-    if (!is.null(attr(tic, "errortext")))

-        stop("Couldn't read total ion current")

-    

-    scanindex <- netCDFVarInt(ncid, "scan_index")

-    if (!is.null(attr(scanindex, "errortext")))

-        stop("Couldn't read scan indecies")

-    

+    scanindex <- netCDFVarInt(ncid, "scan_index")   

     pointValues <- netCDFMSPoints(ncid, scanindex)

-    if (!is.null(attr(pointValues, "errortext")))

-        stop("Couldn't read mass/intensity values")

     startTimeStamp <- netCDFAttText(ncid, "netcdf_file_date_time_stamp")

     return(list(rt = rt, tic = tic, scanindex = scanindex, 

@@ -215,21 +174,9 @@ netCDFRunInfo <- function(ncid) {

 netCDFInstrumentInfo <- function(ncid) {

     imodel <- netCDFVarText(ncid, "instrument_name")

-    if (!is.null(attr(imodel, "errortext")))

-        stop("Couldn't read instrument_name")

-

     imanufacturer <- netCDFVarText(ncid, "instrument_mfr")

-    if (!is.null(attr(imodel, "errortext")))

-        stop("Couldn't read instrument_mfr")

-

     iionisation <- netCDFAttText(ncid, "test_ionization_mode")

-    if (!is.null(attr(iionisation, "errortext")))

-        stop("Couldn't read test_ionization_mode")

-

     idetector <- netCDFAttText(ncid, "test_detector_type")

-    if (!is.null(attr(idetector, "errortext")))

-        stop("Couldn't read test_detector_type")

-

     ianalyzer <- NA

     return(list(model = imodel, manufacturer=imanufacturer,

@@ -121,12 +121,9 @@ ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \

 RHDF5_LIBS=`echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave`

 endif

-NC_CFLAGS=`nc-config --cflags || /bin/true`

-NC_LIBS=-L/opt/lib/hdf5-18/lib/ `nc-config --libs || echo " -lnetcdf "`

+MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o

-MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o

-

-OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS) rampR.o R_init_mzR.o

+OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS) rampR.o 

 ## Generate dependency files

 #DEPFLAGS = -MT $@ -MMD -MP 

deleted file mode 100644

@@ -1,19 +0,0 @@

-#include <R_ext/Rdynload.h>

-#include "rnetCDF.h"

-

-static const R_CMethodDef cMethods[] = {

-    {"NetCDFStrError", (DL_FUNC) &NetCDFStrError, 3},

-    {"NetCDFOpen", (DL_FUNC) &NetCDFOpen, 3},

-    {"NetCDFClose", (DL_FUNC) &NetCDFClose, 2},

-    {"NetCDFVarID", (DL_FUNC) &NetCDFVarID, 4},

-    {"NetCDFVarLen", (DL_FUNC) &NetCDFVarLen, 4},

-    {"NetCDFVarDouble", (DL_FUNC) &NetCDFVarDouble, 4},

-    {"NetCDFVarInt", (DL_FUNC) &NetCDFVarInt, 4},

-    {"NetCDFMSPoints", (DL_FUNC) &NetCDFMSPoints, 7},

-    {NULL, NULL, 0}

-};

-

-void R_init_mzR(DllInfo * info)

-{

-    R_registerRoutines(info, cMethods, NULL, NULL, NULL);

-}

deleted file mode 100755

@@ -1,140 +0,0 @@

-#include <string.h>

-#include "rnetCDF.h"

-

-void NetCDFStrError(const int *ncerr, const int *len, char *errortext[]) {

-

-    strncpy(errortext[0], nc_strerror(*ncerr), *len);

-}

-

-void NetCDFOpen(const char *fileName[], int *ncid, int *status) {

-    

-    *status = nc_open(fileName[0], NC_NOWRITE, ncid);

-}

-

-void NetCDFClose(const int *ncid, int *status) {

-    

-    *status = nc_close(*ncid);

-}

-

-void NetCDFVarID(const int *ncid, const char *varName[], int *varid, int *status) {

-    

-    *status = nc_inq_varid(*ncid, varName[0], varid);

-}

-

-void NetCDFVarLen(const int *ncid, const int *varid, int *len, int *status) {

-    

-    int    ndims, dimids[NC_MAX_VAR_DIMS], i;

-    size_t dimLen;

-    

-    if ((*status = nc_inq_varndims(*ncid, *varid, &ndims)))

-        return;

-    

-    if ((*status = nc_inq_vardimid(*ncid, *varid, dimids)))

-        return;

-    

-    *len = 1;

-    for (i = 0; i < ndims; i++) {

-        if ((*status = nc_inq_dimlen(*ncid, dimids[i], &dimLen)))

-            return;

-        *len *= dimLen;

-    }

-}

-

-void NetCDFVarDouble(const int *ncid, const int *varid, double *data, int *status) {

-    

-    int    varLen, i;

-    double scaleFactor, addOffset;

-    size_t attLen;

-    

-    NetCDFVarLen(ncid, varid, &varLen, status);

-    if (*status)

-        return;

-    

-    if ((*status = nc_get_var_double(*ncid, *varid, data)))

-        return;

-    

-    if (!nc_inq_att(*ncid, *varid, "scale_factor", NULL, &attLen))

-        if (attLen == 1 && !nc_get_att_double(*ncid, *varid, "scale_factor", &scaleFactor) && scaleFactor != 1)

-            for (i = 0; i < varLen; i++)

-                data[i] *= scaleFactor;

-    

-    if (!nc_inq_att(*ncid, *varid, "add_offset", NULL, &attLen))

-        if (attLen == 1 && !nc_get_att_double(*ncid, *varid, "add_offset", &addOffset) && addOffset != 0)

-            for (i = 0; i < varLen; i++)

-                data[i] += addOffset;

-}

-

-void NetCDFVarInt(const int *ncid, const int *varid, int *data, int *status) {

-    

-    int    varLen;

-    

-    NetCDFVarLen(ncid, varid, &varLen, status);

-    if (*status)

-        return;

-    

-    *status = nc_get_var_int(*ncid, *varid, data);

-}

-

-void NetCDFVarText(const int *ncid, const int *varid, char **data, int *status) {

-    

-    int    varLen;

-    

-    NetCDFVarLen(ncid, varid, &varLen, status);

-    if (*status)

-        return;

-

-    *status = nc_get_var_text(*ncid, *varid, data[0]);

-}

-

-void NetCDFGlobalAttribute(const int *ncid, const char **attname, char **data, int *status) {

-    

-    size_t    attLen;

-

-    *status = nc_inq_attlen (*ncid, NC_GLOBAL, attname[0], &attLen);

-    if (*status)

-        return;

-    

-    *status = nc_get_att_text(*ncid, NC_GLOBAL, attname[0], data[0]);

-}

-

-void NetCDFMSPoints(const int *ncid, const int *scanNumber, 

-                    const int *scanIndex, const int *pointNumber, 

-                    double *massValues, double *intensityValues, int *status) {

-    

-    int    varid, i, j, scanLen;

-    double tmpMass, tmpIntensity;

-    

-    *status = nc_inq_varid(*ncid, "mass_values", &varid);

-    if (*status)

-        return;

-    

-    NetCDFVarDouble(ncid, &varid, massValues, status);

-    if (*status)

-        return;

-    

-    *status = nc_inq_varid(*ncid, "intensity_values", &varid);

-    if (*status)

-        return;

-    

-    NetCDFVarDouble(ncid, &varid, intensityValues, status);

-    if (*status)

-        return;

-    

-    for (i = 0; i < *scanNumber-1; i++)

-        if (scanIndex[i+1] - scanIndex[i] > 1) 

-            if (massValues[scanIndex[i]] < massValues[scanIndex[i]+1])

-                return;

-    

-    for (i = 0; i < *scanNumber; i++) {

-        scanLen = (i < *scanNumber - 1) ? scanIndex[i+1] - scanIndex[i] :

-                                          *pointNumber - scanIndex[i];

-        for (j = 0; j < scanLen/2; j++) {

-            tmpMass = massValues[scanIndex[i]+j];

-            tmpIntensity = intensityValues[scanIndex[i]+j];

-            massValues[scanIndex[i]+j] = massValues[scanIndex[i]+scanLen-1-j];

-            intensityValues[scanIndex[i]+j] = intensityValues[scanIndex[i]+scanLen-1-j];

-            massValues[scanIndex[i]+scanLen-1-j] = tmpMass;

-            intensityValues[scanIndex[i]+scanLen-1-j] = tmpIntensity;

-        }

-    }

-}

deleted file mode 100644

@@ -1,23 +0,0 @@

-#include <netcdf.h>

-

-void NetCDFStrError(const int *ncerr, const int *len, char *errortext[]);

-

-void NetCDFOpen(const char *fileName[], int *ncid, int *status);

-

-void NetCDFClose(const int *ncid, int *status);

-

-void NetCDFVarID(const int *ncid, const char *varName[], int *varid, int *status);

-

-void NetCDFVarLen(const int *ncid, const int *varid, int *len, int *status);

-

-void NetCDFVarDouble(const int *ncid, const int *varid, double *data, int *status);

-

-void NetCDFVarInt(const int *ncid, const int *varid, int *data, int *status);

-

-void NetCDFVarText(const int *ncid, const int *varid, char **data, int *status);

-

-void NetCDFGlobalAttribute(const int *ncid, const char **attname, char **data, int *status);

-

-void NetCDFMSPoints(const int *ncid, const int *scanNumber,

-                    const int *scanIndex, const int *pointNumber,

-                    double *massValues, double *intensityValues, int *status);