NAME
Bio::BioStudio::Mask
VERSION
Version 2.10
DESCRIPTION
BioStudio functions
AUTHOR
Sarah Richardson <smrichardson@lbl.gov>.
CONSTRUCTORS
new
Title : new
Function:
Returns : a new Bio::BioStudio::Mask object
Args :Masking functions
add_to_mask()
Given an array reference full of SeqFeatures, fills the mask
remove_from_mask()
insert_sequence()
remove_sequence()
find_deserts()
find_overlaps()
what_overlaps()
what_objects_overlap()
overlap_extents()
occlusion
count_features()
count_features_in_range
features_in_range
feature_objects_in_range
range_string
ACCESSORS
seqid
len
feature_index
PRIVATE
_sanity_check
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.