NAME

       TFBS::DB::FlatFileDir - interface to a database of pattern matrices stored as a collection
       of flat files in a dedicated directory

SYNOPSIS

       ·   creating a database object by connecting to the existing directory

               my $db = TFBS::DB::FlatFileDir->connect("/home/boris/MatrixDir");

       ·   retrieving a TFBS::Matrix::* object from the database

               # retrieving a PFM by ID
               my $pfm = $db->get_Matrix_by_ID('M00079','PFM');

               #retrieving a PWM by name
               my $pwm = $db->get_Matrix_by_name('NF-kappaB', 'PWM');

       ·   retrieving a set of matrices as a TFBS::MatrixSet object according to various criteria

               # retrieving a set of PWMs from a list of IDs:
               my @IDlist = ('M0019', 'M0045', 'M0073', 'M0101');
               my $matrixset = $db->get_MatrixSet(-IDs => \@IDlist,
                                                  -matrixtype => "PWM");

               # retrieving a set of ICMs from a list of names:
               my @namelist = ('p50', 'p53', 'HNF-1'. 'GATA-1', 'GATA-2', 'GATA-3');
               my $matrixset = $db->get_MatrixSet(-names => \@namelist,
                                                  -matrixtype => "ICM");

               # retrieving a set of all PFMs in the database
               my $matrixset = $db->get_MatrixSet(-matrixtype => "PFM");

       ·   creating a new FlatFileDir database in a new directory:

               my $db = TFBS::DB::JASPAR2->create("/home/boris/NewMatrixDir");

       ·   storing a matrix in the database:

               #let $pfm is a TFBS::Matrix::PFM object
               $db->store_Matrix($pfm);

DESCRIPTION

       TFBS::DB::FlatFileDir is a read/write database interface module that retrieves and stores
       TFBS::Matrix::* and TFBS::MatrixSet objects in a set of flat files in a dedicated
       directory. It has a very simple structure and can be easily set up manually if desired.

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       preceded with an underscore.

   new
        Title   : new
        Usage   : my $db = TFBS::DB::FlatFileDir->new(%args);
        Function: the formal constructor for the TFBS::DB::FlatFileDir object;
                  most users will not use it - they will use specialized
                  I<connect> or I<create> constructors to create a
                  database object
        Returns : a TFBS::DB::FlatFileDir object
        Args    : -dir       # the directory containing flat files

   connect
        Title   : connect
        Usage   : my $db = TFBS::DB::FlatFileDir->connect($directory);
        Function: Creates a database object that retrieves TFBS::Matrix::*
                  object data from or stores it in an existing directory
        Returns : a TFBS::DB::FlatFileDir object
        Args    : ($directory)
                   The name of the directory (possibly with fully qualified
                   path).

   create
        Title   : create
        Usage   : my $newdb = TFBS::DB::FlatFileDir->create($new_directory);
        Function: connects to the database server, creates a new directory,
                  sets up a FlatFileDir database and returns a database
                  object that interfaces the database
        Returns : a TFBS::DB::FlatFileDir object
        Args    : ($new_directory)
                   The name of the directory to create
                   (possibly with fully qualified path).

   get_Matrix_by_ID
        Title   : get_Matrix_by_ID
        Usage   : my $pfm = $db->get_Matrix_by_ID('M00034', 'PFM');
        Function: fetches matrix data under the given ID from the
                  database and returns a TFBS::Matrix::* object
        Returns : a TFBS::Matrix::* object; the exact type of the
                  object depending on the second argument (allowed
                  values are 'PFM', 'ICM', and 'PWM'); returns undef if
                  matrix with the given ID is not found
        Args    : (Matrix_ID, Matrix_type)
                  Matrix_ID is a string; Matrix_type is one of the
                  following: 'PFM' (raw position frequency matrix),
                  'ICM' (information content matrix) or 'PWM' (position
                  weight matrix)
                  If Matrix_type is omitted, a PWM is retrieved by default.

   get_Matrix_by_name
        Title   : get_Matrix_by_name
        Usage   : my $pfm = $db->get_Matrix_by_name('HNF-1', 'PWM');
        Function: fetches matrix data under the given name from the
                  database and returns a TFBS::Matrix::* object
        Returns : a TFBS::Matrix::* object; the exact type of the object
                  depending on the second argument (allowed values are
                  'PFM', 'ICM', and 'PWM')
        Args    : (Matrix_name, Matrix_type)
                  Matrix_name is a string; Matrix_type is one of the
                  following:
                  'PFM' (raw position frequency matrix),
                  'ICM' (information content matrix) or
                  'PWM' (position weight matrix)
                  If Matrix_type is omitted, a PWM is retrieved by default.
        Warning : According to the current JASPAR2 data model, name is
                  not necessarily a unique identifier. In the case where
                  there are several matrices with the same name in the
                  database, the function fetches the first one and prints
                  a warning on STDERR. You have been warned.

   store_Matrix
        Title   : store_Matrix
        Usage   : $db->store_Matrix($matrixobj);
        Function: Stores the contents of a TFBS::Matrix::DB object in the database
        Returns : 0 on success; $@ contents on failure
                  (this is too C-like and may change in future versions)
        Args    : ($matrixobj) # a TFBS::Matrix::* object

   delete_Matrix_having_ID
        Title   : delete_Matrix_having_ID
        Usage   : $db->delete_Matrix_with_ID('M00045');
        Function: Deletes the matrix having the given ID from the database
        Returns : 0 on success; $@ contents on failure
                  (this is too C-like and may change in future versions)
        Args    : (ID)
                  A string
        Comment : Yeah, yeah, 'delete_Matrix_having_ID' is a stupid name
                  for a method, but at least it should be obviuos what it does.