ProtPsm documentation.

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

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

To handle a combination of site matrices and/or their corresponding sequence
matches (instances). This object inherits from Bio::Matrix::PSM::ProtMatrix, so
you can methods from that class. It may hold also an array of
Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these
through Bio::Matrix::PSM::ProtPsm->instances method (see below). To some
extent this is an expanded ProtMatrix object, holding data from analysis that
also deal with sequence matches of a particular matrix. This does not make too much sense to me 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.

Title : new
Usage : my $psm = Bio::Matrix::PSM::ProtPsm->new(
-pS => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
-pF => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
-pT => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
-pN => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
-pK => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
-pY => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pE => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
-pV => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
-pQ => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
-pM => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
-pC => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pL => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
-pA => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
-pW => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pP => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
-pH => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
-pD => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
-pR => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
-pI => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
-pG => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
-IC => $ic,
-sites => $istes,
-width => $width,
-e_val => $e_val,
-instances => $instances,
}
Function: Creates a new Bio::Matrix::PSM::ProtPsm object Throws : Example : Returns : Bio::Matrix::PSM::Psm object Args : hash

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)

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 an epty list 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...)

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

sub new {

    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;
    my $self = $class->SUPER::new(@args);
    $self->{'_annotation'} = {};  #Init from Annotation::Collection
    $self->_typemap(Bio::Annotation::TypeManager->new()); #same
    ($self->{instances})=$self->_rearrange(['INSTANCES'], @args);
    return $self;

}

sub header {

    my $self = shift;
    return  if ($self->{end});
    my %header;
    if (@_) {my $key=shift; return $self->{$key}; }
    foreach my $key (@Bio::Matrix::PSM::ProtPsm::HEADER) {
	$header{$key}=$self->{$key};
    }
    return %header;

}

sub matrix {

   my $self = shift;

   if (@_) {
      my $matrix = shift;
      my @alphabet = $self->alphabet;

      foreach my $char (@alphabet) {
         $self->{"log$char"}  = $matrix->{"log$char"};
         $self->{"prob$char"} = $matrix->{"prob$char"};
      }
      $self->{IC}    = $matrix->IC;
      $self->{e_val} = $matrix->e_val;
      $self->{id}    = $matrix->id;
    }

    return $self;
}

1;

}

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and other Bioperl modules. Send your comments and suggestions preferably
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.

new	Description	Code
instances	Description	Code
header	Description	Code
matrix	Description	Code