Bio::Matrix::PSM PsmHeaderI
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::PSM::PsmHeaderI
Package variables
No package variables defined.
Included modules
Bio::Matrix::PSM::IO
Bio::Matrix::PSM::InstanceSite
Bio::Matrix::PSM::Psm
base qw ( Bio::Matrix::PSM::PsmI )
strict
Synopsis
 use Bio::Matrix::PSM::IO;
 #Obtain an Bio::Matrix::PSM::IO object:
 my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'mast');

 #Get some general data about the file you are parsing:
 my $release=$psmIO->release;
 my $version=$psmIO->version;

 print "This analysis was performed using MAST version $version, release $release\n";

 #Now let's see what are the consensus sequences of the motifs fed as an input:
 my %seq=$psmIO->seq;

 #let's cycle through all consensus sequences now:

 foreach my $id ($psmIO->hid) {
   print "Motif $id is \t",$seq{$id},"\n";
 }

  #Finally look at the stuff we do not parse:
  my @inputfile=grep(/datafile/i,$psmIO->unstructured);
Description
Generally you should not use this object directly, you can access the
information through a PSM driver (See Bio::Matrix::PSM::IO). It is
handling the header data from a PSM file which may be very
different. This means that some of the methods will return undef
naturally, because this information is not present in the file which
is parsed. Some important data might be left over in the unstructured
part, and you might have to parse it yourself. I will try to
'structure' this header more in the near future.
Methods
seqDescriptionCode
hidDescriptionCode
lengthDescriptionCode
instancesDescriptionCode
weightsDescriptionCode
unstructured
No description
Code
versionDescriptionCode
revisionDescriptionCode
_checkDescriptionCode
Methods description
seqcode    nextTop
 Title   : seq
 Usage   : my %seq= $header->seq();
 Function: Returns the sequence data as a hash, indexed by a 
           sequence ID (motif id or accession number)
           In case the input data is a motif it would return the 
           consenus seq for each of them (mast).
 Throws  :
 Example :
 Returns :  hash
 Args    :
hidcodeprevnextTop
 Title   : hid
 Usage   : my @ids= $header->hid();
 Function: Returns array with the motif/instance ids
 Throws  :
 Example :
 Returns :  array
 Args    :
lengthcodeprevnextTop
 Title   : length
 Usage   : my %length= $header->length();
 Function: Returns the length of the input sequence or motifs as a hash, indexed
           by a sequence ID (motif id or accession number)
 Throws  :
 Example :
 Returns :  hash
 Args    :
instancescodeprevnextTop
 Title   : instances
 Usage   : my %instances= $header->length();
 Function: Returns the instance, used  as a hash, indexed
           by a sequence ID (motif id or accession number)
 Throws  :
 Example :
 Returns :  hash of Bio::Matrix::PSM::InstanceSite objects
 Args    :
weightscodeprevnextTop
 Title   : weights
 Usage   : my %weights= $header->weights();
 Function: Returns the weights of the input sequence as a hash, indexed
           by a sequence ID
 Throws  :
 Example :
 Returns :  hash
 Args    :
versioncodeprevnextTop
 Title   : version
 Usage   : my $version= $header->version;
 Function: Returns the version of the file being parsed if such exists
 Throws  :
 Example :
 Returns :  string
 Args    :
revisioncodeprevnextTop
 Title   : revision
 Usage   : my $revision= $header->revision;
 Function: Returns the revision of the file being parsed if such exists
 Throws  :
 Example :
 Returns :  string
 Args    :
_checkcodeprevnextTop
 Title   : _check
 Usage   : if ($self->_check('weights') { #do something} else {return 0;}
 Function: Checks if the method called is aplicable to the file format
 Throws  :
 Example :
 Returns :  boolean
 Args    :  string
Methods code
seqdescriptionprevnextTop
sub seq {
     my $self = shift;
    $self->throw_not_implemented();
}
hiddescriptionprevnextTop
sub hid {
     my $self = shift;
    $self->throw_not_implemented();
}
lengthdescriptionprevnextTop
sub length {
     my $self = shift;
    $self->throw_not_implemented();
}
instancesdescriptionprevnextTop
sub instances {
     my $self = shift;
    $self->throw_not_implemented();
}
weightsdescriptionprevnextTop
sub weights {
     my $self = shift;
    $self->throw_not_implemented();
}
unstructureddescriptionprevnextTop
sub unstructured {
     my $self = shift;
    $self->throw_not_implemented();
}
versiondescriptionprevnextTop
sub version {
     my $self = shift;
    $self->throw_not_implemented();
}
revisiondescriptionprevnextTop
sub revision {
     my $self = shift;
    $self->throw_not_implemented();
}
_checkdescriptionprevnextTop
sub _check {
     my $self = shift;
    $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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:
  http://bugzilla.open-bio.org/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop
newTop
 Title   : new
 Usage   : my $header= new Bio::Matrix::PSM::PsmHeader
            ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
              -instances=>\%instances, -header=>\@header, -type=>'mast');
 Function: Creates a new Bio::Matrix::PSM::PsmHeader object
 Throws  :
 Example :
 Returns :  Bio::Matrix::PSM::PsmHeaderI object
 Args    :  hash
unstucturedTop
 Title   : unstuctured
 Usage   : my @unstructured= $header->unstuctured();
 Function: Returns the unstructured data in the header as an array, one line per
           array element, all control symbols are removed with \W
 Throws  :
 Example :
 Returns :   array
 Args    :