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

 Package: affxparser

-Version: 1.23.2

-Date: 2011-02-15

+Version: 1.23.3

+Date: 2011-02-22

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan

 Maintainer: Kasper Daniel Hansen <[email protected]>

@@ -8,6 +8,6 @@ Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR).

 FusionDetails: Fusion SDK v1.1.0

 License: LGPL (>= 2)

 Depends: R (>= 2.6.0)

-Suggests: R.utils, AffymetrixDataTestFiles

+Suggests: R.utils (>= 1.6.3), AffymetrixDataTestFiles

 LazyLoad: yes

 biocViews: Infrastructure, DataImport

@@ -82,7 +82,7 @@ convertCel <- function(filename, outFilename, readMap=NULL, writeMap=NULL, versi

   if (!is.null(newChipType)) {

     newChipType <- as.character(newChipType);

     if (nchar(newChipType) == 0) {

-      stop("Argument 'newChipType' cannot be a empty string.");

+      stop("Argument 'newChipType' cannot be an empty string.");

     }

   }

@@ -109,7 +109,7 @@ convertCel <- function(filename, outFilename, readMap=NULL, writeMap=NULL, versi

   hdr <- cel$header;

   if (!is.null(newChipType)) {

     if (verbose) {

-      cat("Updating chip type from '", hdr$chiptype, "' to '", 

+      cat("Updating the chip type label from '", hdr$chiptype, "' to '", 

                                               newChipType, "'.\n", sep="");

     }

@@ -41,97 +41,128 @@

     header <- strsplit(header, split="\n")[[1]];

   }

+

+  # Extract the "head" and the "tail" of the DAT header

+  pattern <- "([^\024]*)(\024.*)";

+  head <- gsub(pattern, "\\1", header);

+  tail <- gsub(pattern, "\\2", header);

+

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

   # [123456789012345678900123456789001234567890]

   # "[5..65534]  NA06985_H_tH_B5_3005533:",      ????

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

   pattern <- "^([^:]*):(.*)$";

-  bfr <- gsub(pattern, "\\1", header);

-  header2 <- gsub(pattern, "\\2", header);

-

-  bfr <- trim(bfr);                           # Example: "[12..40151]  Fetal 3"

-  pattern <- "^([^]]*])[ ]*(.*)[ ]*";

-  pixelRange <- gsub(pattern, "\\1", bfr);

-  sampleName <- gsub(pattern, "\\2", bfr);

-  if (identical(pixelRange, sampleName)) {

-    stop("Internal error: Failed to extract 'pixelRange' and 'sampleName' from DAT header.  They became identical: ", pixelRange);

-  }

+  if (regexpr(pattern, head) != -1) {

+    bfr <- gsub(pattern, "\\1", header);

+    header2 <- gsub(pattern, "\\2", header);

+    bfr <- trim(bfr);             # Example: "[12..40151]  Fetal 3"

+    if (nchar(bfr) > 0) {

+      pattern <- "^([^ ]*])[ ]*(.*)[ ]*";

+      pixelRange <- gsub(pattern, "\\1", bfr);

+      sampleName <- gsub(pattern, "\\2", bfr);

+      if (identical(pixelRange, sampleName)) {

+        stop("Internal error: Failed to extract 'pixelRange' and 'sampleName' from DAT header.  They became identical: ", pixelRange);

+      }

+    } else {

+      pixelRange <- "";

+      sampleName <- "";

+    }

-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-  # Parse the DAT header

-  #

-  # 1. Number of pixels per row (padded with spaces), preceded with 

-  #    "CLS=". char[9]

-  # 2. Number of rows in the image (padded with spaces), preceded with 

-  #    "RWS=".char[9]

-  # 3. Pixel width in micrometers (padded with spaces), preceded with 

-  #    "XIN=" char[7]

-  # 4. Pixel height in micrometers (padded with spaces), preceded with 

-  #    "YIN=". char[7]

-  # 5. Scan speed in millimeters per second (padded with spaces), preceded 

-  #    with "VE=". char[6]

-  # 6. Temperature in degrees Celsius (padded with spaces). If no temperature

-  #    was set then the entire field is empty. char[7]

-  # 7. Laser power in milliwatts or microwatts (padded with spaces). char[4]

-  # 8. Date and time of scan (padded with spaces). char[18]

-  #

-  # Example:

-  # [123456789012345678900123456789001234567890] (See above)

-  # "CLS=8714 ",

-  # "RWS=8714 ",

-  # "XIN=1  ",

-  # "YIN=1  ",

-  # "VE=30 ",

-  # "       ",

-  # "2.0 ",

-  # "01/14/04 14:26:57 "

-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-  len <- c(9,9,7,7,6,7,4,18,220);

-  ends <- cumsum(len);

-  starts <- ends - len + 1;

-  header <- substring(header2, starts, ends);

-  header <- trim(header);

-

-  # Store the last field

-  bfr <- header[9];

-

-  header <- list(

-    pixelRange = pixelRange,

-    sampleName = sampleName,

-    CLS = gsub("^CLS=(.*)", "\\1", header[1]),

-    RWS = gsub("^RWS=(.*)", "\\1", header[2]),

-    XIN = gsub("^XIN=(.*)", "\\1", header[3]),

-    YIN = gsub("^YIN=(.*)", "\\1", header[4]),

-    VE = gsub("^VE=(.*)", "\\1", header[5]),

-    scanTemp = header[6],

-    laserPower = header[7],

-    scanDate = header[8]

-  )

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    # Parse the DAT header

+    #

+    # 1. Number of pixels per row (padded with spaces), preceded with 

+    #    "CLS=". char[9]

+    # 2. Number of rows in the image (padded with spaces), preceded with 

+    #    "RWS=".char[9]

+    # 3. Pixel width in micrometers (padded with spaces), preceded with 

+    #    "XIN=" char[7]

+    # 4. Pixel height in micrometers (padded with spaces), preceded with 

+    #    "YIN=". char[7]

+    # 5. Scan speed in millimeters per second (padded with spaces), preceded 

+    #    with "VE=". char[6]

+    # 6. Temperature in degrees Celsius (padded with spaces). If no temperature

+    #    was set then the entire field is empty. char[7]

+    # 7. Laser power in milliwatts or microwatts (padded with spaces). char[4]

+    # 8. Date and time of scan (padded with spaces). char[18]

+    #

+    # Example:

+    # [123456789012345678900123456789001234567890] (See above)

+    # "CLS=8714 ",

+    # "RWS=8714 ",

+    # "XIN=1  ",

+    # "YIN=1  ",

+    # "VE=30 ",

+    # "       ",

+    # "2.0 ",

+    # "01/14/04 14:26:57 "

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    len <- c(9,9,7,7,6,7,4,18,220);

+    ends <- cumsum(len);

+    starts <- ends - len + 1;

+    header <- substring(header2, starts, ends);

+    header <- trim(header);

+  

+    # Store the last field

+    bfr <- header[9];

+  

+    header <- list(

+      pixelRange = pixelRange,

+      sampleName = sampleName,

+      CLS = gsub("^CLS=(.*)", "\\1", header[1]),

+      RWS = gsub("^RWS=(.*)", "\\1", header[2]),

+      XIN = gsub("^XIN=(.*)", "\\1", header[3]),

+      YIN = gsub("^YIN=(.*)", "\\1", header[4]),

+      VE = gsub("^VE=(.*)", "\\1", header[5]),

+      scanTemp = header[6],

+      laserPower = header[7],

+      scanDate = header[8]

+    );

+

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    # The 'bfr' field:

+    #

+    # "There are several sub-fields in this field. The first sub field is the 

+    #  scanner ID, sometimes followed by a number, followed by three spaces. 

+    #  If the scanner ID is absent, the field consists of four spaces.

+    #

+    # Example:

+    # [123456789012345678900123456789001234567890] (????)

+    # "50101230  M10   \024  \024 Hind240.1sq \024  \024  \024  \024  

+    # \024  \024  \024  \024  \024 6"

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    # 0x14 == 024

+    pattern <- "^([^\024]*)[ ]*(\024.*)$";

+    scannerInfo <- gsub(pattern, "\\1", bfr);

+    scannerInfo <- trim(scannerInfo);

+    bfr <- gsub(pattern, "\\2", bfr);

+  

+  # Not locale safe: pattern <- "^([a-zA-Z0-9]*)[ ]*([a-zA-Z0-9]*)[ ]*";

+    pattern <- "^([abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0-9]*)[ ]*([abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0-9]*)[ ]*";

+    header$scanner <- list(

+        id = gsub(pattern, "\\1", scannerInfo),

+      type = gsub(pattern, "\\2", scannerInfo)

+    );

+  } else {

+    # TO DO: Make these NAs to have the correct storage modes

+    naValue <- as.character(NA);

+    naValue <- "";

+    header <- list(

+      pixelRange = naValue,

+      sampleName = naValue,

+      CLS = naValue,

+      RWS = naValue,

+      XIN = naValue,

+      YIN = naValue,

+      VE = naValue,

+      scanTemp = naValue,

+      laserPower = naValue,

+      scanDate = naValue,

+      scanner = list(id=naValue, type=naValue)

+    );

+  }

-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-  # The 'bfr' field:

-  #

-  # "There are several sub-fields in this field. The first sub field is the 

-  #  scanner ID, sometimes followed by a number, followed by three spaces. 

-  #  If the scanner ID is absent, the field consists of four spaces.

-  #

-  # Example:

-  # [123456789012345678900123456789001234567890] (????)

-  # "50101230  M10   \024  \024 Hind240.1sq \024  \024  \024  \024  

-  # \024  \024  \024  \024  \024 6"

-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-  # 0x14 == 024

-  pattern <- "^([^\024]*)[ ]*(\024.*)$";

-  scannerInfo <- gsub(pattern, "\\1", bfr);

-  scannerInfo <- trim(scannerInfo);

-  bfr <- gsub(pattern, "\\2", bfr);

-

-# Not locale safe: pattern <- "^([a-zA-Z0-9]*)[ ]*([a-zA-Z0-9]*)[ ]*";

-  pattern <- "^([abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0-9]*)[ ]*([abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0-9]*)[ ]*";

-  header$scanner <- list(

-      id = gsub(pattern, "\\1", scannerInfo),

-    type = gsub(pattern, "\\2", scannerInfo)

-  )

+  bfr <- tail;

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

   #  Next are 10 structured comment fields. Each field is preceded by the 

@@ -268,6 +299,13 @@

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

 # HISTORY:

+# 2011-02-22

+# o ROBUSTNESS/BUG FIX: The internal .unwrapDatHeaderString() would

+#   throw "Internal error: Failed to extract 'pixelRange' and 'sampleName' 

+#   from DAT header.  They became identical: ..." in case the DAT header

+#   of the CEL file did not contain all fields.  The function has now

+#   been updated to be more forgiving and robust so that missing values

+#   are returned for such fields instead.

 # 2007-08-16

 # o BUG FIX: Internal .unwrapDatHeaderString() failed to correctly extract

 #   'pixelRange' and 'sampleName' from DAT header.

@@ -1,6 +1,15 @@

 Package: affxparser

 ===================

+Version: 1.23.3 [2011-02-22]

+o ROBUSTNESS/BUG FIX: The internal .unwrapDatHeaderString() would

+  throw "Internal error: Failed to extract 'pixelRange' and 'sampleName' 

+  from DAT header.  They became identical: ..." in case the DAT header

+  of the CEL file did not contain all fields.  The function has now

+  been updated to be more forgiving and robust so that missing values

+  are returned for such fields instead. 

+

+

 Version: 1.23.2 [2011-02-15]

 o DOCUMENTATION: Added a clarification to the help page on

   'Cell coordinates and cell indices' that the convention 

@@ -71,7 +71,7 @@

    zero-based coordinates in the CDF file.

    All methods of the \pkg{affxparser} package make use of these

-   (x,y) coordinates, and some methods makes it possible to read

+   (x,y) coordinates, and some methods make it possible to read

    them as well.  However, it is much more common that the methods

    return cell indices \emph{calculated} from the (x,y) coordinates

    as explained above.