Sarah Richardson > Bio-BioStudio-1.05 > Bio::BioStudio::RestrictionEnzyme::Store

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Module Version: 1.05   Source   Latest Release: Bio-BioStudio-2.00

NAME ^

Bio::BioStudio::RestrictionEnzyme::Store

VERSION ^

Version 1.05

DESCRIPTION ^

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.

AUTHOR ^

Sarah Richardson <notadoctor@jhu.edu>

CONSTRUCTORS ^

new

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.

FUNCTIONS ^

load

Load the database from the dumpfile (defined during the call to new)

search

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.

cull

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.

screen

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.

Accessor functions ^

dbh

Returns the database handle linked to the MySQL database.

name

Returns the name of the database.

user

Returns the username used to access the MySQL database.

dumpfile

Returns the path to the file used to quickload the MySQL database.

enzyme_definitions

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

Private functions ^

_initialize

Creates the only table in the database.

_table_definition

Private: the SQL definition of the table that stores enzyme information

COPYRIGHT AND LICENSE ^

Copyright (c) 2011, BioStudio developers All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

* Neither the name of the Johns Hopkins nor the names of the developers may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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