DESIGN ISSUES¶

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 because 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.

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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:

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new¶

 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

instances¶

 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)

header¶

 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...)

matrix¶

 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