new¶

 Title   : new
 Usage   : DEPRECATED - for backward compatibility only
           Use connect() or create() instead

connect¶

 Title   : connect
 Usage   : my $db =
            TFBS::DB::JASPAR2->connect("dbi:mysql:DATABASENAME:HOSTNAME",
                                        "USERNAME",
                                        "PASSWORD");
 Function: connects to the existing JASPAR2-type database and
           returns a database object that interfaces the database
 Returns : a TFBS::DB::JASPAR2 object
 Args    : a standard database connection triplet
           ("dbi:mysql:DATABASENAME:HOSTNAME",  "USERNAME", "PASSWORD")
           In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
           use the actual values. PASSWORD and USERNAME might be
           optional, depending on the user acces permissions for
           the database server.

create¶

 Title   : create
 Usage   : my $newdb =
            TFBS::DB::JASPAR2->create("dbi:mysql:NEWDATABASENAME:HOSTNAME",
                                      "USERNAME",
                                      "PASSWORD");
 Function: connects to the database server, creates a new JASPAR2-type database and returns a database
           object that interfaces the database
 Returns : a TFBS::DB::JASPAR2 object
 Args    : a standard database connection triplet
            ("dbi:mysql:NEWDATABASENAME:HOSTNAME",  "USERNAME", "PASSWORD")
           In place of NEWDATABASENAME, HOSTNAME, USERNAME and
           PASSWORD use the actual values. PASSWORD and USERNAME
           might be optional, depending on the users acces permissions
           for the database server.

dbh¶

 Title   : dbh
 Usage   : my $dbh = $db->dbh();
           $dbh->do("UPDATE matrix_data SET name='ADD1' WHERE NAME='SREBP2'");
 Function: returns the DBI database handle of the MySQL database
           interfaced by $db; THIS IS USED FOR WRITING NEW METHODS
           FOR DIRECT RELATIONAL DATABASE MANIPULATION - if you
           have write access AND do not know what you are doing,
           you can severely  corrupt the data
           For documentation about database handle methods, see L<DBI>
 Returns : the database (DBI) handle of the MySQL JASPAR2-type
           relational database associated with the TFBS::DB::JASPAR2
           object
 Args    : none

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.

get_MatrixSet¶

 Title   : get_MatrixSet
 Usage   : my $matrixset = $db->get_MatrixSet(%args);
 Function: fetches matrix data under for all matrices in the database
           matching criteria defined by the named arguments
           and returns a TFBS::MatrixSet object
 Returns : a TFBS::MatrixSet object
 Args    : This method accepts named arguments:
           -IDs        # a reference to an array of IDs (strings)
           -names      # a reference to an array of
                       #  transcription factor names (string)
           -classes    # a reference to an array of
                       #  structural class names (strings)
           -species    # a reference to an array of
                       #   Latin species names (strings)
           -sysgroups  # a reference to an array of
                       #  higher taxonomic categories (strings)

           -matrixtype # a string, 'PFM', 'ICM' or 'PWM'
           -min_ic     # float, minimum total information content
                       #   of the matrix

The five arguments that expect list references are used in database query formulation: elements within lists are combined with 'OR' operators, and the lists of different types with 'AND'. For example,

    my $matrixset = $db->(-classes => ['TRP_CLUSTER', 'FORKHEAD'],
                          -species => ['Homo sapiens', 'Mus musculus'],
                          -matrixtype => 'PWM');

gives a set of PWMs whose (structural clas is 'TRP_CLUSTER' OR 'FORKHEAD') AND (the species they are derived from is 'Homo sapiens' OR 'Mus musculus').

The -min_ic filter is applied after the query in the sense that the matrices profiles with total information content less than specified are not included in the set.

store_Matrix¶

 Title   : store_Matrix
 Usage   : $db->store_Matrix($pfm);
 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    : (PFM_object)
           A TFBS::Matrix::PFM object
 Comment : this is an experimental method that is not 100% bulletproof;
           use at your own risk

store_MatrixSet¶

 Title   : store_MatrixSet
 Usage   : $db->store_Matrix($matrixset);
 Function: Stores the TFBS::DB::PFM object that are part of a
           TFBS::MatrixSet object into the database
 Returns : 0 on success; $@ contents on failure
           (this is too C-like and may change in future versions)
 Args    : (MatrixSet_object)
           A TFBS::MatrixSet object
 Comment : THIS METHOD IS NOT YET IMPLEMENTED

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.