NAME
Bio::BioStudio::Diff
VERSION
Version 2.10
DESCRIPTION
An object that allows the comparison of two Bio::BioStudio::Chromosome objects.
AUTHOR
Sarah Richardson <smrichardson@lbl.gov>.
CONSTRUCTOR METHOD
new
DESTROY
COMPARISON METHODS
compare_dbs
compare_features
compare_feature_sources
compare_feature_types
compare_feature_lengths
compare_feature_orientations
compare_feature_scores
compare_feature_phases
compare_feature_attributes
compare_feature_annotations
compare_feature_sequences
compare_feature_translations
compare_comments
verify_newseq
ACCESSOR METHODS
oldchr
newchr
checktrx
aligntrx
alignseq
checkseq
BLAST_factory
PRIVATE
_make_bl2seq_factory
Returns a Bio::Tools::Run::StandAloneBlastPlus object that can be used to run BLAST bl2seq queries
COPYRIGHT AND LICENSE
Copyright (c) 2015, 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.
* The names of Johns Hopkins, the Joint Genome Institute, the Joint BioEnergy Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the BioStudio developers may not 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.