Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation

SYNOPSIS

         # See Bio::Matrix::PSM::IO for detailed documentation on how to use
         # PSM parsers

DESCRIPTION

       Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM
       sequence matches

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://github.com/bioperl/bioperl-live/issues

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::PsmHeader 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 @hid= $header->hid();
        Function: Returns array with the motif 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->instances();
        Function: Returns the info about the input data, contained in the header
        Throws  :
        Example :
        Returns : hash
        Args    :

   weight
        Title   : weight
        Usage   : my %weights= $header->weight();
        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    :

   release
        Title   : release
        Usage   : my $release= $header->release;
        Function: Returns the release 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