Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation # See Bio::Matrix::PSM::IO for detailed documentation on how to use # PSM parsers Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches

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new
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::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 undef;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string