git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@74592 bc3139a8-67e5-0310-9ffc-ced21a209358
H Bengtsson authored on 20/03/2013 03:34:49
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@19352 bc3139a8-67e5-0310-9ffc-ced21a209358
Henrik Bengtsson authored on 19/08/2006 07:53:55
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+########################################################################/-Rdoc TURNED OFF-** |
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+# @RdocFunction .readCelHeaderV3 |
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+# |
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+# @title "Read the header of a CEL v3 (ASCII) file" |
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+# |
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+# \description{
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+# @get "title". |
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+# } |
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+# |
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+# @synopsis |
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+# |
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+# \arguments{
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+# \item{con}{An open and readable @connection.}
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+# } |
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+# |
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+# \value{
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+# Returns a named @list structure. |
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+# } |
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+# |
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+# \details{
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+# When the header is read, the file pointer is at the line after the |
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+# header. Empty lines should be expected before the intensity section. |
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+# This function does not make use of Fusion SDK. |
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+# } |
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+# |
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+# @author |
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+# |
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+# @keyword IO |
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+# @keyword File |
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+# @keyword internal |
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+#**-Rdoc TURNED OFF-/####################################################################### |
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+.readCelHeaderV3 <- function(con, ...) {
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+ trim <- function(s, ...) {
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+ s <- gsub("^[ \t]*", "", s);
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+ s <- gsub("[ \t]*$", "", s);
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+ s; |
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+ } |
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+ |
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+ # Read "[CEL]" |
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+ while (TRUE) {
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+ tag <- trim(readLines(con, n=1)); |
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+ if (!identical(tag, "")) |
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+ break; |
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+ } |
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+ if (!identical(tag, "[CEL]")) {
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+ stop("Could not read CEL v3 file header. File format error: File does not start with [CEL]: ", tag);
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+ } |
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+ |
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+ # Read version |
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+ version <- trim(readLines(con, n=1)); |
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+ if (!identical(version, "Version=3")) {
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+ stop("Could not read CEL v3 file header. Not a version 3 file: ", version);
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+ } |
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+ |
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+ # Read "[HEADER]" |
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+ while (TRUE) {
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+ tag <- trim(readLines(con, n=1)); |
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+ if (!identical(tag, "")) |
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+ break; |
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+ } |
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+ if (!identical(tag, "[HEADER]")) {
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+ stop("Could not read CEL v3 file header. Expected HEADER section, but got: ", tag);
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+ } |
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+ |
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+ # Read header fields |
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+ header <- list( |
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+ version = as.integer(3) |
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+ ); |
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+ while (TRUE) {
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+ field <- trim(readLines(con, n=1)); |
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+ if (identical(field, "")) |
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+ break; |
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+ field <- unlist(strsplit(field, split="=")); |
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+ key <- field[1]; |
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+ value <- paste(field[-1], collapse="="); |
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+ header[[key]] <- value; |
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+ } |
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+ |
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+ # Fields to be converted to integers |
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+ intFields <- c("Cols", "Rows", "TotalX", "TotalY",
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+ "OffsetX", "OffsetY", "swapXY"); |
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+ # Ad hoc, but the "Axis" fields are sometimes misspelled. |
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+ axisFields <- grep("^Axis[-]*(i|I)nvert(X|Y)$", names(header), value=TRUE);
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+ intFields <- c(intFields, axisFields); |
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+ for (ff in intersect(names(header), intFields)) {
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+ header[[ff]] <- as.integer(header[[ff]]); |
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+ } |
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+ |
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+ # Vector fields |
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+ for (ff in grep("GridCorner", names(header))) {
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+ value <- header[[ff]]; |
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+ value <- unlist(strsplit(value, split=" ")); |
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+ value <- trim(value); |
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+ value <- as.integer(value); |
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+ header[[ff]] <- value; |
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+ } |
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+ |
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+ header; |
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+} # .readCelHeaderV3() |
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+ |
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+ |
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+############################################################################ |
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+# HISTORY: |
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+# 2006-07-10 |
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+# o Created from .readCelHeaderV3(). |
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+############################################################################ |