Browse code

Spell corrections using the 'spelling' package

Henrik Bengtsson authored on 23/10/2018 02:36:30
Showing 1 changed files
... ...
@@ -7,7 +7,7 @@
7 7
 # 
8 8
 # \description{
9 9
 #   @get "title".
10
-#   \emph{This method is not indended to be used explicitly. 
10
+#   \emph{This method is not intended to be used explicitly. 
11 11
 #   To write a CDF, use @see "writeCdf" instead.}
12 12
 # }
13 13
 # 
Browse code

o Added an Authors@R field to DESCRIPTION. o Recompiled the Rdoc-to-Rd help files using R 1.13.0, i.e. R.oo::compileRdoc().

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
Showing 1 changed files
... ...
@@ -27,7 +27,7 @@
27 27
 #   Returns nothing.
28 28
 # }
29 29
 #
30
-# @author
30
+# @author "HB"
31 31
 #
32 32
 # \seealso{
33 33
 #   This method is called by @see "writeCdf".
Browse code

o Added missing Rd files. o Converged the method API to the same camel case changes that James Bullard did in the devel branch for those methods that we happened to work on in parallel. o Will commit added/modified changes to the devel branch too.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@22355 bc3139a8-67e5-0310-9ffc-ced21a209358

Henrik Bengtsson authored on 01/02/2007 19:02:01
Showing 1 changed files
... ...
@@ -1,13 +1,53 @@
1
+#########################################################################/**
2
+# @RdocFunction writeCdfHeader
3
+#
4
+# @title "Writes a CDF header"
5
+#
6
+# @synopsis 
7
+# 
8
+# \description{
9
+#   @get "title".
10
+#   \emph{This method is not indended to be used explicitly. 
11
+#   To write a CDF, use @see "writeCdf" instead.}
12
+# }
13
+# 
14
+# \arguments{
15
+#   \item{con}{An open @connection to which nothing has been written.}
16
+#   \item{cdfHeader}{A CDF header @list structure.}
17
+#   \item{unitNames}{A @character @vector of all unit names.}
18
+#   \item{qcUnitLengths}{An @integer @vector of all the number of bytes
19
+#     in each of the QC units.}
20
+#   \item{unitLengths}{An @integer @vector of all the number of bytes
21
+#     in each of the (ordinary) units.}
22
+#   \item{verbose}{An @integer specifying how much verbose details are
23
+#     outputted.}
24
+# }
25
+# 
26
+# \value{
27
+#   Returns nothing.
28
+# }
29
+#
30
+# @author
31
+#
32
+# \seealso{
33
+#   This method is called by @see "writeCdf".
34
+#   See also @see "writeCdfQcUnits" and @see "writeCdfUnits".
35
+# }
36
+# 
37
+# @keyword "file"
38
+# @keyword "IO"
39
+# @keyword "internal"
40
+#*/#########################################################################
1 41
 writeCdfHeader <- function(con, cdfHeader, unitNames, qcUnitLengths, unitLengths, verbose=0) {
2 42
   if (verbose >= 1)
3 43
     cat("  Writes CDF header and unit names...\n");
4 44
 
5 45
   .initializeCdf(con = con,
6
-                 nunits = cdfHeader$nunits,
7
-                 nqcunits = cdfHeader$nqcunits,
8
-                 refseq = cdfHeader$refseq,
9
-                 nrows = cdfHeader$nrows,
10
-                 ncol = cdfHeader$ncols,
46
+                 nRows = cdfHeader$nrows,
47
+                 nCols = cdfHeader$ncols,
48
+                 nUnits = cdfHeader$nunits,
49
+                 nQcUnits = cdfHeader$nqcunits,
50
+                 refSeq = cdfHeader$refseq,
11 51
                  unitnames = unitNames,
12 52
                  qcUnitLengths = qcUnitLengths,
13 53
                  unitLengths = unitLengths
... ...
@@ -20,6 +60,8 @@ writeCdfHeader <- function(con, cdfHeader, unitNames, qcUnitLengths, unitLengths
20 60
 
21 61
 ############################################################################
22 62
 # HISTORY:
63
+# 2007-02-01 /HB
64
+# o Added Rdoc comments.
23 65
 # 2007-01-10 /HB
24 66
 # o Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits().  With
25 67
 #   these it is now possible to build up the CDF in chunks.
Browse code

o Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits(). These are all used by writeCdf(). They also make it possible to write a CDF in chunks in order to for instance convertCdf() in constant memory. These functions still need to be documented.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@21888 bc3139a8-67e5-0310-9ffc-ced21a209358

Henrik Bengtsson authored on 09/01/2007 08:44:30
Showing 1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,62 @@
1
+writeCdfHeader <- function(con, cdfHeader, unitNames, qcUnitLengths, unitLengths, verbose=0) {
2
+  if (verbose >= 1)
3
+    cat("  Writes CDF header and unit names...\n");
4
+
5
+  .initializeCdf(con = con,
6
+                 nunits = cdfHeader$nunits,
7
+                 nqcunits = cdfHeader$nqcunits,
8
+                 refseq = cdfHeader$refseq,
9
+                 nrows = cdfHeader$nrows,
10
+                 ncol = cdfHeader$ncols,
11
+                 unitnames = unitNames,
12
+                 qcUnitLengths = qcUnitLengths,
13
+                 unitLengths = unitLengths
14
+  );
15
+
16
+  if (verbose >= 1)
17
+    cat("  Writes CDF header and unit names...done\n");
18
+} # writeCdfHeader()
19
+
20
+
21
+############################################################################
22
+# HISTORY:
23
+# 2007-01-10 /HB
24
+# o Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits().  With
25
+#   these it is now possible to build up the CDF in chunks.
26
+# o Removed obsolete arguments 'addName' and 'addPositions' and all related
27
+#   code.  Internal variable 'positions' is not needed anymore. 
28
+#   There are no more seek():s in the code.
29
+# o Removed obsolete .writeCdfUnit2().
30
+# o Now only every 1000th unit (instead of 100th) is reported. It is now
31
+#   also a count down.
32
+# 2006-12-18 /KS
33
+# o Make global replacement "block" -> "group" to maintain consistency
34
+#   with other code, pursuant to communication from KH.
35
+# 2006-10-25 /HB (+KS)
36
+# o BUG FIX: .initializeCdf() was writing false file offset for QC units
37
+#   when the number QC nunits were zero.  This would core dump readCdfNnn().
38
+# 2006-09-21 /HB
39
+# o BUG FIX: The 'atom' and 'indexpos' fields were swapped.
40
+# o Now suppressing warnings "writeChar: more characters requested..." in
41
+#   writeCdf().
42
+# 2006-09-11 /HB
43
+# o BUG FIX: nrows & ncols were swapped in the CDF header.
44
+# 2006-09-09 /HB
45
+# o Updated writeCdf() has been validate with compareCdfs() on a few arrays.
46
+# o With the below "optimizations" writeCdf() now writes Hu6800.CDF with
47
+#   units in 130s compared to 140s.
48
+# o Now initializeCdf() dumps all unit names at once by first building a
49
+#   raw vector.  This is now much faster than before.
50
+# o Now writeCdf() does not seek() around in the file anymore.  This should
51
+#   speed up writing at least a bit.
52
+# o Made some optimization, which speeds up the writing a bit.  Jumping
53
+#   around in the file with seek() is expensive and should be avoided.
54
+# o Rename writeUnit() to writeCdfUnit() and same for the QC function.
55
+# o Added more verbose output and better errror messages for writeCdf().
56
+# 2006-09-07 /HB
57
+# o Maybe initalizeCdf(), writeUnit(), and writeQcUnit() should be made
58
+#   private functions of this package.
59
+# o Removed textCdf2binCdf() skeleton. See convertCdf() instead.
60
+# o Updated writeCdf() such that the connection is guaranteed to be closed
61
+#   regardless.
62
+############################################################################