[Seqinr-commits] r1733 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2010-03-06 18:53:29 +0100 (Sat, 06 Mar 2010)
New Revision: 1733

Modified:
   pkg/man/read.alignment.Rd
Log:
New quality control routine check

Modified: pkg/man/read.alignment.Rd
===================================================================
--- pkg/man/read.alignment.Rd	2010-03-06 17:52:39 UTC (rev 1732)
+++ pkg/man/read.alignment.Rd	2010-03-06 17:53:29 UTC (rev 1733)
@@ -91,10 +91,21 @@
 
  }
 \examples{
-mase <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
-clustal <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
-phylip <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
-msf <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
-fasta <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+mase.res   <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
+clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
+phylip.res  <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
+msf.res      <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
+fasta.res    <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+
+#
+# Quality control routine sanity checks:
+#
+
+data(mase); stopifnot(identical(mase, mase.res))
+data(clustal); stopifnot(identical(clustal, clustal.res))
+data(phylip); stopifnot(identical(phylip, phylip.res))
+data(msf); stopifnot(identical(msf, msf.res))
+data(fasta); stopifnot(identical(fasta, fasta.res))
+
 }