An object that stores the database handle for a MySQL database full of restriction enzyme recognition sites - usually corresponding to the sites found on a chromosome that is being prepared for segmentation.
Sarah Richardson <email@example.com>
There are two required arguments:
-name the name of the database -enzyme_definitions This is a reference to a hash that has L<Bio::GeneDesign::RestrictionEnzyme> objects as values. This hash can be obtained from the GeneDesign function define_sites.
The other arguments are optional:
-user The user name for the MySQL database -pass The password for the MySQL database -file Path to a dumpfile that is used to quickload the MySQL database. -create A flag that causes creation of the database. Otherwise, an attempt is made to open a handle to an existing database.
Load the database from the dumpfile (defined during the call to new)
Performs a search of the database.
-name search by the name field -left a lower bound for the search on the start field -right an upper bound for the search on the start field -enzyme search by the id of the enzyme (BamHI, BssSI etc)
Returns an array reference containing Bio::BioStudio::RestrictionEnzyme objects.
Removes entries from the database.
Arguments: a reference to a list of numbers that correspond to primary ids in the database; all rows whose primary key is in the list will be removed.
Marks entries in the database as ineligible (sets the eligible field to "no").
Arguments: a reference to a list of numbers that correspond to primary ids in the database; all rows whose primary key is in the list will be marked ineligible.
Returns the database handle linked to the MySQL database.
Returns the name of the database.
Returns the username used to access the MySQL database.
Returns the path to the file used to quickload the MySQL database.
The hash of generic Bio::GeneDesign::RestrictionEnzyme objects that are used to bootstrap creation of Bio::BioStudio::RestrictionEnzyme objects. This hash can be created by calling Bio::GeneDesign::RestrictionEnzymes::define_sites
Creates the only table in the database.
Private: the SQL definition of the table that stores enzyme information
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