\name{Globals Variables}
\alias{globals}
\title{Globals variables on Gene sequences}


\description{
  There are two ways to store sequences in GeneR:
  \itemize{
    \item In a C adapted class (buffers) that stores in addition some globals
    variables, like working strand, size of original sequence and so
    on.
  
    It is usefull when, for example, we have to work on a subset of a
    whole chromosome (i.e. a gene). In this case it will be worthwhile
    to load only the gene in R. Nevertheless, it will remain easy to
    associate positions on chromosome and positions on gene \dots

    \item As a character string, the more logical way to store short sequences
    like "ATGTCGTG".  It concerns all functions like "strxxx" (\link{strComp},
    \link{strReadFasta} etc.).
   
%    extract positions on genome, gene

%    correspondances between addresses on genome and
%    addresses on gene, or address from the reverse\dots

   % A complete description on this C class is  given in page  \code{\link{globals}}.
  }
}


\details{
  When GeneR load a subset of a larger sequence stored in a bank file,
%  (by example a gene from a whole chromosome).
  it will store the following informations in the C adapted class
  (buffers, by default 100 buffers than can be extended if necessary):
  \itemize{
    \item subsequence (i.e. the succession of A,T,G,C).
    \item postions of the extremities of the subsequence  in the
    master sequence
    \item size of the whole sequence in the bank file
    \item name of the sequence
    }
  
    For specific purposes as renaming a sequence, all these variables
    can be viewed and carefully changed at any time  (here functions
    \code{\link{getAccn}} and \code{\link{setAccn}}).
    
    Several sequences can be stored
    simultaneously and called by their buffer number.

    Strand is another global variable which can be set and viewed 
    (functions \code{\link{getStrand}} and \code{\link{setStrand}}). It
    is used as input parameter in many functions to analyze
    complementary strand. It was designed to avoid doing explicitly the
    complement of the loaded strand then to store it in a buffer with,
    as consequence, loss of the informations linked to the master sequence.
    
  
    We have defined 3 types of addresses on a subsequence extracted from
    a master sequence:

  \itemize{
    \item Absolute addresses i.e. addresses on the master sequence, from the 5' end
    of the input strand refered as forward (noted A)
    \item Real addresses, i.e.  addresses on the master sequence, from the 5'
    end of one of strands (noted R)
    \item Relative addresses, i.e.  addresses on working subsequence,
    from the 5' end of one of strands (noted T).
  }
  
  Let's show an example, if we read sequence from 11 to 20 from
  a gene of size 40:

  \preformatted{
  Strand 0  (Forward strand)
  1         11       20                  40  Absolute (A) 
  1         11       20                  40  Real (R) 
            1        10                      Relative (T)
  xxxxxxxxxxATGTGTCGTAxxxxxxxxxxxxxxxxxxxx
            10       1                       Relative (T)
  40        30       21                  1   Real (R)
  1         11       20                  40  Absolute (A)
  Strand 1  (Reverse strand)

  }
  Obviously, when an entire sequence is stored, real and relative
  addresses will be the same.
    
  Although all functions using positions need and return absolute
  addresses, 6 functions allow to convert R, A, T into any other type
  (functions \code{\link{RtoA}, \link{RtoT}, \link{AtoR},
    \link{AtoT}, \link{TtoR}, \link{TtoA}}).
  
  A global variable \code{strand} is used to convert positions
  (see  \code{\link{setStrand}}  \code{\link{getStrand}}).
	
  
}

\seealso{
  \code{\link{AtoT}},
  \code{\link{AtoR}},
  \code{\link{RtoA}},
  \code{\link{RtoT}},
  \code{\link{TtoA}},
  \code{\link{TtoR}},
  \code{\link{setStrand}},
  \code{\link{getStrand}},
  \code{\link{getParam}},
  \code{\link{setParam}},
  \code{\link{getAccn}},
  \code{\link{setAccn}}

}


\examples{

## Make a dummy sequence
s <- "xxxxxxxxxxATGTGTCGTAxxxxxxxxxxxxxxxxxxxx"
placeString(s)
writeFasta(file="toto.fa")

indexFasta("toto.fa")
readFasta("toto.fa",from=11,to=20)

getParam()
## $begin 
## [1] 11
## $size
## [1] 40
## $strand
## [1] 0
## [...]

## With strand = 0 
TtoA(c(1,10))
##[1] 10 19

TtoR(c(1,10))
##[1] 10 19

}

\keyword{utilities}