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

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...)

perl v5.32.1                                       2021-08-15                        Bio::Matrix::PSM::PsmI(3pm)

       Email skirov@utk.edu

       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.

   DESIGNISSUES
       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 because 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.

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

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

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

         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 below.