Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies

SYNOPSIS

         use Bio::Matrix::PSM::IO;

         # To get a Psm object from a file use the Psm parser:
         my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file);

         # Now go through all entities in the file with next_psm, which
         # returns a Psm object see Bio::Matrix::PSM::IO for detailed
         # documentation (matrix predictions or matrix sequence matches or
         # both):

         while (my $psm=$psmIO->next_psm) {
          my %psm_header=$psm->header;
          my $ic=$psm_header{IC};
          my $sites=$psm_header{sites};
          my $width=$psm_header{width};
          my $score=$psm_header{e_val};
          my $IUPAC=$psm->IUPAC;
          my $instances=$psm->instances;
          foreach my $instance (@{$instances}) {
            my $id=$instance->primary_id;
            #Do something with the id
           }
          }

         # or create from memmory:
         my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
                                             -id=>$id,
                                             -instances=>$instances, -e_val=>$e_val,
                                             -IC=>$ic, -width=>$width, -sites=>$sites)

         # where pA through pG are the respective frequencies of the matrix (see also
         # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory,
         # except for
         #-instances (reference to an array of Bio::Matrix::PSM::InstanceSite objects)
         # which is documented bellow.

DESCRIPTION

       Supposed to handle a combination of site matrices and/or their corresponding sequence
       matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can
       use the respective methods. It may hold also an array of Bio::Matrix::PSM::InstanceSite
       object, but you will have to retrieve these through Bio::Matrix::PSM::Psm->instances
       method (see below). To some extent this is an expanded SiteMatrix object, holding data
       from analysis that also deal with sequence matches of a particular matrix.

   DESIGN ISSUES
       This design is a bit of a compromise, so it might be a temporary solution I am mixing PSM
       with PSM sequence matches Though they are very closely related, I am not satisfied by the
       way this is implemented here.  Heikki suggested different objects when one has something
       like meme But does this mean we have to write a different objects for mast, meme,
       transfac, theiresias, etc.?  To me the best way is to return SiteMatrix object + arrray of
       InstanceSite objects and then mast will return undef for SiteMatrix and transfac will
       return undef for InstanceSite. Probably I cannot see some other design issues that might
       arise from such approach, but it seems more straightforward.  Hilmar does not like this
       beacause it is an exception from the general BioPerl rules Should I leave this as an
       option?  Also the header rightfully belongs the driver object, and could be retrieved as
       hashes.  I do not think it can be done any other way, unless we want to create even one
       more object with very unclear content.

SEE ALSO

       Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::transfac,
       Bio::Matrix::PSM::InstanceSite

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Stefan Kirov

       Email skirov@utk.edu

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

   new
        Title   : new
        Usage   : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
                                                      -pT=>\@pT,-id=>$id,
                                                      -instances=>$instances,
                                                      -e_val=>$e_val,
                                                      -IC=>$ic, -width=>$width,
                                                      -sites=>$sites)
        Function: Creates a new Bio::Matrix::PSM::Psm object
        Throws  :
        Example :
        Returns :  Bio::Matrix::PSM::Psm object
        Args    :  hash

   instances
        Title   : instances
        Usage   :   my @instances=@{$psm->instances};
        Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects)
                   associated with the Psm object
        Throws  :
        Example :
        Returns :  array reference (Bio::Matrix::PSM::InstanceSite objects)
        Args    :  array reference (Bio::Matrix::PSM::InstanceSite objects)

   matrix
        Title   :  matrix
        Usage   :  my $matrix=$psm->matrix;
        Function:  Gets/sets the SiteMatrix related information
        Throws  :
        Example :
        Returns :  Bio::Matrix::PSM::SiteMatrix objects
        Args    :  Bio::Matrix::PSM::SiteMatrix objects

   header
        Title   : header
        Usage   :  my %header=$psm->header;
                   my $ic=$psm->header('IC');
        Function: Gets the general information, common for most files, dealing
                  with PSM such as information content (IC), score (e-value,
                  etc.), number of sites (sites) and width. This list may
                  expand. The current list should be in
                  @Bio::Matrix::PSM::Psm::HEADER. Returns undef if an argument
                  is supplied that is not in @Bio::Matrix::PSM::meme::HEADER.
        Throws  :
        Example :
        Returns :  hash or string
        Args    :  string (IC, e_val...)