wrong warning in gap.inspect

[Lars Skjærven]

> gaps <- gap.inspect(aln)
Warning message:
In gap.inspect(aln) : Taking $xyz component (NOT $ali)
> aln$xyz
NULL

[Barry Grant]

I have committed a change where we now will take the $xyz component if a 3dalign object is the input (as stated in the warning message) and the $ali component if a non '3dalign' class list object is provided (as in the example above).

I think this is sensible but I see that it could be confusing. I will leave this issue open until others chime in.

files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE)
pdbs <- pdbaln(files)
aln <- read.fasta("aln.fa")

g1 <- gap.inspect(aln)
g3 <- gap.inspect(pdbs)
Warning message:
In gap.inspect(pdbs) :
  Taking $xyz component (NOT $ali for which you should use 'gap.inspect(x$ali)')
> dim(g1$bin)
[1]   2 168
> dim(g3$bin)
[1]   2 504

[Barry Grant]

BUGFIX: gap.inspect() take $xyz component of '3dalign' objects by default

Also changed warning() message. See Issue #86

→ <<cset 42538b24c485>>

[Lars Skjærven]

jolly good