NAME

Bio::BioStudio::Chunk

VERSION

Version 1.05

DESCRIPTION

A chunk is a region of designed DNA between 6k and 10k long; it will contain Bio::GeneDesign::BuildingBlock objects, and will be contained within Bio::BioStudio::Megachunk objects. Chunks are typically flanked by unique Bio::BioStudio::RestrictionEnzyme objects.

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>

CONSTRUCTORS

new

All arguments are optional:

-name      The name of the chunk

-number    The number of the chunk in its megachunk

-prevcand  A L<Bio::BioStudio::RestrictionEnzyme> object corresponding to
           the site at the three prime end of the chunk

-usedenzymes  

-usedoverhangs  

-enzlist  

-bkupenzlist
         
-enzyme   A L<Bio::BioStudio::RestrictionEnzyme> object corresponding to
          the site at the five prime end of the chunk

FUNCTIONS

Accessor functions

prevcand

enzyme

name

used_enzymes

used_overhangs

bkupenzlist

enzlist

number

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.