NAME

       Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file

SYNOPSIS

        use Bio::Matrix::PSM::IO;
        #Obtain an Bio::Matrix::PSM::IO object:
        my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$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.

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

APPENDIX

   new
        Title   : new
        Usage   : my $header= Bio::Matrix::PSM::PsmHeader->new
                   ( -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

   seq
        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    :

   hid
        Title   : hid
        Usage   : my @ids= $header->hid();
        Function: Returns array with the motif/instance ids
        Throws  :
        Example :
        Returns :  array
        Args    :

   length
        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    :

   instances
        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    :

   weights
        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    :

   unstuctured
        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    :

   version
        Title   : version
        Usage   : my $version= $header->version;
        Function: Returns the version of the file being parsed if such exists
        Throws  :
        Example :
        Returns :  string
        Args    :

   revision
        Title   : revision
        Usage   : my $revision= $header->revision;
        Function: Returns the revision of the file being parsed if such exists
        Throws  :
        Example :
        Returns :  string
        Args    :

   _check
        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