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

 Type: Package

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

        (mass spectrometry data)

-Version: 2.1.9

+Version: 2.1.10

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

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

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

@@ -1,3 +1,8 @@

+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

+

 CHANGES IN VERSION 2.1.9

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

  o Fix a compiler warning on OSX in the pep_XML serialiser

@@ -108,63 +108,52 @@ setMethod("isInitialized",

           signature="mzRnetCDF",

           function(object) return(object@backend > 0))

-## setMethod("runInfo",

-##           signature="mzRnetCDF",

-##           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)

-##           })

+setMethod("runInfo",

+           signature="mzRnetCDF",

+          function(object) 

+              return(netCDFRunInfo(object@backend)))

-## setMethod("instrumentInfo",

-##           signature="mzRnetCDF",

-##           function(object) 

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

-

+setMethod("instrumentInfo",

+          signature="mzRnetCDF",

+          function(object) 

+              return(netCDFInstrumentInfo(object@backend)))

-## setMethod("manufacturer",

-##           signature="mzRnetCDF",

-##           function(object) {

-##             info <- instrumentInfo(object)           

-##             return(info$manufacturer)

-##           })

-## setMethod("model",

-##           signature="mzRnetCDF",

-##           function(object) {

-##             info <- instrumentInfo(object)           

-##             return(info$model)

-##           })

+setMethod("manufacturer",

+          signature="mzRnetCDF",

+          function(object) {

+            info <- instrumentInfo(object)           

+            return(info$manufacturer)

+          })

-## setMethod("ionisation",

-##           signature="mzRnetCDF",

-##           function(object) {

-##             info <- instrumentInfo(object)           

-##             return(info$ionisation)

-##           })

+setMethod("model",

+          signature="mzRnetCDF",

+          function(object) {

+            info <- instrumentInfo(object)           

+            return(info$model)

+          })

-## setMethod("analyzer",

-##           signature="mzRnetCDF",

-##           function(object) {

-##             info <- instrumentInfo(object)           

-##             return(info$analyzer)

-##           })

+setMethod("ionisation",

+          signature="mzRnetCDF",

+          function(object) {

+            info <- instrumentInfo(object)           

+            return(info$ionisation)

+          })

-## setMethod("detector",

-##           signature="mzRnetCDF",

-##           function(object) {

-##             info <- instrumentInfo(object)           

-##             return(info$detector)

-##           })

+setMethod("analyzer",

+          signature="mzRnetCDF",

+          function(object) {

+            info <- instrumentInfo(object)           

+            return(info$analyzer)

+          })

+setMethod("detector",

+          signature="mzRnetCDF",

+          function(object) {

+            info <- instrumentInfo(object)           

+            return(info$detector)

+          })

 setMethod("show",

           signature="mzRnetCDF",

@@ -123,6 +123,33 @@ netCDFVarInt <- function(ncid, var) {

        PACKAGE = "mzR")$data

 }

+netCDFVarText <- function(ncid, var) {

+

+    if (is.character(var))

+        var <- netCDFVarID(ncid, 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

+}

+

+netCDFAttText <- function(ncid, att) {

+

+    .C("NetCDFGlobalAttribute",

+       as.integer(ncid),

+       as.character(att),

+       data = character(1),

+       status = integer(1),

+       PACKAGE = "mzR")$data

+}

+

+

 netCDFMSPoints <- function(ncid, scanIndex) {

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

@@ -168,3 +195,42 @@ netCDFRawData <- function(ncid) {

                 mz = pointValues$massValues,

                 intensity = pointValues$intensityValues))

 }

+

+netCDFRunInfo <- function(ncid) {

+

+    ncraw <- netCDFRawData(ncid)

+

+    return(list(scanCount = length(ncraw$scanindex),

+                lowMz = min (ncraw$mz),

+                highMz = max (ncraw$mz),

+                dStartTime = min (ncraw$rt),

+                dEndTime = max (ncraw$rt),

+                msLevels = NA))

+}

+

+

+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,

+                ionisation = iionisation, detector = idetector,

+                analyzer = ianalyzer))

+}

+

@@ -17,6 +17,6 @@ BUILT_RCPP_VERSION = package_version("@BUILT_RCPP_VERSION@")

       }

       require2 <- require

       require2("methods", character.only = TRUE, quietly = TRUE)

-      loadRcppModules()

+#      loadRcppModules()

       Sys.setenv("HDF5_DISABLE_VERSION_CHECK"=2)

 }

@@ -93,6 +93,12 @@ MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o Rc

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

+

+

+

+MZROBJECTS=rnetCDF.o 

+OBJECTS= $(MZROBJECTS) 

+

 ##

 ## R complains about assert(), hence -D_NODEBUG

 ##  http://www.gamedev.net/topic/555511-is-there-a-way-to-only-disable-boost-debug-checks/

@@ -75,6 +75,28 @@ void NetCDFVarInt(const int *ncid, const int *varid, int *data, int *status) {

     *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) {

@@ -14,6 +14,10 @@ void NetCDFVarDouble(const int *ncid, const int *varid, double *data, int *statu

 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);