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

 CHANGES IN VERSION 2.15.1

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

- o Fix type (see https://github.com/sneumann/mzR/pull/162)

+ o Fix typo (see https://github.com/sneumann/mzR/pull/162)

+ o New .hasSpectra and .hasChromatograms private function (see

+   https://github.com/lgatto/MSnbase/issues/343)

 CHANGES IN VERSION 2.15.0

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

@@ -169,3 +169,13 @@ setMethod("show",

             invisible(NULL)

           })

+setMethod("chromatograms", "mzRnetCDF", function(object, chrom)

+    chromatogram(object, chrom))

+setMethod("chromatogram", "mzRnetCDF", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram()

+})

+setMethod("chromatogramHeader", "mzRnetCDF", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram_header()

+})

@@ -163,3 +163,14 @@ setMethod("show",

 setMethod("isolationWindow", "mzRramp",

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

+

+setMethod("chromatograms", "mzRramp", function(object, chrom)

+    chromatogram(object, chrom))

+setMethod("chromatogram", "mzRramp", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram()

+})

+setMethod("chromatogramHeader", "mzRramp", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram_header()

+})

@@ -40,3 +40,59 @@ setMethod("isolationWindow", "character",

     x <- lapply(x, base::unique)

     any(sapply(x, function(xx) nrow(xx) > 1))

 }

+

+

+.hasSpectra <- function(x) {

+    close_after <- FALSE

+    if (is.character(x) && file.exists(x)) {

+        x <- mzR::openMSfile(x)

+        ## Ensure we are closing the file later

+        close_after <- TRUE

+    }

+    stopifnot(inherits(x, "mzR"))

+    len <- length(x)

+    if (close_after)

+        close(x)

+    return(as.logical(len))

+}

+

+#' Create return data for MS backends not supporting chromatographic data. This

+#' function is supposed to be called by the chromatogram(s) methods for these

+#' backends

+#'

+#' @author Johannes Rainer

+#'

+#' @noRd

+.empty_chromatogram <- function() {

+    list()

+}

+

+#' Create return data for MS backends not supporting chromatographic data.

+#'

+#' @author Johannes Rainer

+#'

+#' @noRd

+.empty_chromatogram_header <- function() {

+    cn <- c("chromatogramId", "chromatogramIndex", "polarity",

+            "precursorIsolationWindowTargetMZ",

+            "precursorIsolationWindowLowerOffset",

+            "precursorIsolationWindowUpperOffset",

+            "precursorCollisionEnergy", "productIsolationWindowTargetMZ",

+            "productIsolationWindowLowerOffset",

+            "productIsolationWindowUpperOffset")

+    data.frame(matrix(nrow = 0, ncol = length(cn),

+                      dimnames = list(character(), cn)))

+}

+

+.hasChromatograms <- function(x) {

+    close_after <- FALSE

+    if (is.character(x) && file.exists(x)) {

+        x <- mzR::openMSfile(x)

+        close_after <- TRUE

+    }

+    stopifnot(inherits(x, "mzR"))

+    hdr <- chromatogramHeader(x)

+    if (close_after)

+        close(x)

+    as.logical(nrow(hdr))

+}

@@ -58,3 +58,27 @@ test_header <- function() {

   close(cdf)

 }

+

+test_chromatogram <- function() {

+    file <- system.file('cdf/ko15.CDF', package = "msdata")

+    x <- openMSfile(file, backend="netCDF")        

+    suppressWarnings(

+        chr <- chromatogram(x)

+    )

+    checkTrue(length(chr) == 0)

+    suppressWarnings(

+        chr <- chromatograms(x)

+    )

+    checkTrue(length(chr) == 0)

+    close(x)

+}

+

+test_chromatogramHeader <- function() {

+    file <- system.file('cdf/ko15.CDF', package = "msdata")

+    x <- openMSfile(file, backend="netCDF")        

+    suppressWarnings(

+        ch <- chromatogramHeader(x)

+    )

+    checkTrue(nrow(ch) == 0)

+    close(x)

+}

@@ -102,4 +102,32 @@ test_peaks_spectra <- function() {

     p <- peaks(x, 1:10)

     s <- spectra(x, 1:10)

     checkIdentical(p, s)

+    close(x)

 }

+

+test_chromatogram <- function() {

+    library("msdata")

+    f <- proteomics(full.names = TRUE)

+    x <- openMSfile(f[1], backend = "Ramp")

+    suppressWarnings(

+        chr <- chromatogram(x)

+    )

+    checkTrue(length(chr) == 0)

+    suppressWarnings(

+        chr <- chromatograms(x)

+    )

+    checkTrue(length(chr) == 0)

+    close(x)

+}

+

+test_chromatogramHeader <- function() {

+    library("msdata")

+    f <- proteomics(full.names = TRUE)

+    x <- openMSfile(f[1], backend = "Ramp")

+    suppressWarnings(

+        ch <- chromatogramHeader(x)

+    )

+    checkTrue(nrow(ch) == 0)

+    close(x)

+}

+

new file mode 100644

@@ -0,0 +1,20 @@

+test_hasChromatograms <- function() {

+    fl <- system.file("proteomics/MRM-standmix-5.mzML.gz", package = "msdata")

+    x <- mzR::openMSfile(fl, backend = "pwiz")

+    checkTrue(mzR:::.hasChromatograms(x))

+    checkTrue(mzR:::.hasChromatograms(fl))

+    close(x)

+    

+    fl <- system.file("cdf/ko15.CDF", package = "msdata")

+    x <- openMSfile(fl, backend = "netCDF")        

+    suppressWarnings(checkTrue(!mzR:::.hasChromatograms(x)))

+    suppressWarnings(checkTrue(!mzR:::.hasChromatograms(fl)))

+    close(x)

+

+    fl <- system.file("sciex/20171016_POOL_POS_1_105-134.mzML",

+                      package = "msdata")

+    x <- mzR::openMSfile(fl, backend = "pwiz")

+    checkTrue(!mzR:::.hasChromatograms(x))

+    checkTrue(!mzR:::.hasChromatograms(fl))

+    close(x)

+}

@@ -29,6 +29,12 @@

 \alias{chromatogram,mzRpwiz-method}

 \alias{chromatogramHeader,mzRpwiz-method}

 \alias{chromatograms,mzRpwiz-method}

+\alias{chromatogram,mzRramp-method}

+\alias{chromatogramHeader,mzRramp-method}

+\alias{chromatograms,mzRramp-method}

+\alias{chromatogram,mzRnetCDF-method}

+\alias{chromatogramHeader,mzRnetCDF-method}

+\alias{chromatograms,mzRnetCDF-method}

 \alias{tic,mzRpwiz-method}

 \alias{nChrom}

 \alias{chromatogram}

@@ -84,7 +84,7 @@ int RcppPwiz::getLastScan() const {

     SpectrumListPtr slp = msd->run.spectrumListPtr;

     return slp->size();

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return -1;

 }

@@ -93,7 +93,7 @@ int RcppPwiz::getLastChrom() const {

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     return clp->size();

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return -1;

 }

@@ -160,7 +160,7 @@ Rcpp::List RcppPwiz::getInstrumentInfo ( )

         }

       return(instrumentInfo);

     }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return instrumentInfo;

 }

@@ -306,7 +306,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)

       return header;

     }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::DataFrame::create( );

 }

@@ -324,7 +324,7 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( )

         }

       return allScanHeaderInfo ;

     }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::DataFrame::create( );

 }

@@ -362,7 +362,7 @@ Rcpp::List RcppPwiz::getPeakList ( int whichScan )

 				Rcpp::_["peaks"]  = peaks

 				) ;

     }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::List::create( );

 }

@@ -756,10 +756,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )

   if (msd != NULL) {

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     if (clp.get() == 0) {

-      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;

+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");

       return Rcpp::DataFrame::create();

     } else if (clp->size() == 0) {

-      Rcpp::Rcerr << "No available chromatogram info." << std::endl;

+      Rf_warningcall(R_NilValue, "No available chromatogram info.");

       return Rcpp::DataFrame::create();

     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {

       Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);

@@ -783,7 +783,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )

     }

     return(chromatogramsInfo);

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::DataFrame::create( );

 }

@@ -794,10 +794,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh

     CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this...

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     if (clp.get() == 0) {

-      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;

+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");

       return Rcpp::DataFrame::create();

     } else if (clp->size() == 0) {

-      Rcpp::Rcerr << "No available chromatogram info." << std::endl;

+      Rf_warningcall(R_NilValue, "No available chromatogram info.");

       return Rcpp::DataFrame::create();

     }

@@ -821,8 +821,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh

     for (int i = 0; i < N_chrom; i++) {

       int current_chrom = whichChrom[i];

       if (current_chrom < 0 || current_chrom > N) {

+	Rf_warningcall(R_NilValue, "Provided index out of bounds.");

 	Rcpp::Rcerr << "Provided index out of bounds" << std::endl;

-	return Rcpp::DataFrame::create();

       }

       ChromatogramPtr ch = clp->chromatogram(current_chrom - 1, false);

       chromatogramId[i] = ch->id;

@@ -877,18 +877,24 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh

     chromHeader.attr("names") = names;

     return chromHeader;

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::DataFrame::create( );

 }

 Rcpp::DataFrame RcppPwiz::getAllChromatogramHeaderInfo ( ) {

   if (msd != NULL) {

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

+    if (clp.get() == 0) {

+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");

+      return Rcpp::DataFrame::create();

+    }

     int N = clp->size();

-    

-    return getChromatogramHeaderInfo(Rcpp::seq(1, N));

+    if (N > 0) {

+      return getChromatogramHeaderInfo(Rcpp::seq(1, N));

+    } else {

+      Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

+    }

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

   return Rcpp::DataFrame::create( );

 }

@@ -915,7 +921,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh

         }

       int j=0;

-      Rprintf("%d\n",1);

+      //Rprintf("%d\n",1);

       for (int i = 0; i < scanNumbers.size(); i++)

         {

 	  SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);

@@ -939,7 +945,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh

       return(map3d);

     }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return Rcpp::NumericMatrix(0,0);

 }

@@ -947,6 +953,6 @@ string RcppPwiz::getRunStartTimeStamp() {

   if (msd != NULL) {

     return msd->run.startTimeStamp;

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");

   return "";

 }

@@ -55,7 +55,7 @@ Rcpp::StringVector RcppRamp::getFilename (  )

     {

         return filename;

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return filename;

 }

@@ -86,7 +86,7 @@ Rcpp::List RcppRamp::getRunInfo (  )

         }

         return runInfo;

     }

-    Rprintf("Warning: Ramp not yet initialized.\n");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return runInfo;

 }

@@ -130,7 +130,7 @@ Rcpp::List RcppRamp::getInstrumentInfo ( )

         }

         return(instrumentInfo);

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return instrumentInfo;

 }

@@ -200,7 +200,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )

         return  header;

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return Rcpp::List::create( );

 }

@@ -322,7 +322,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )

         }

         return(allScanHeaderInfo);

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return Rcpp::DataFrame::create( );

 }

@@ -361,7 +361,7 @@ Rcpp::List RcppRamp::getPeakList ( int whichScan )

                    Rcpp::_["peaks"]  = peaks

                ) ;

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return Rcpp::List::create( );

 }

@@ -384,7 +384,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh

         }

         // map3d = 0.0;

         int j=0;

-        Rprintf("%d\n",1);

+        //Rprintf("%d\n",1);

         for (int i = 0; i < scanNumbers.size(); i++)

         {

             rampPeakList *pl = ramp->getPeakList( scanNumbers[i] );

@@ -415,7 +415,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh

         }

         return(map3d);

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return Rcpp::NumericMatrix(0,0);

 }

@@ -425,7 +425,7 @@ int RcppRamp::getLastScan() const

     {

         return ramp->getLastScan();

     }

-    Rprintf("Warning: Ramp not yet initialized.\n ");

+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");

     return -1;

 }