bio::search::hsp::hspfactory(3pm) [debian man page]
Bio::Search::HSP::HSPFactory(3pm) User Contributed Perl Documentation Bio::Search::HSP::HSPFactory(3pm)NAME
Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects
SYNOPSIS
use Bio::Search::HSP::HSPFactory;
my $factory = Bio::Search::HSP::HSPFactory->new();
my $resultobj = $factory->create(@args);
DESCRIPTION
This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO
parser depending on what format report we are parsing.
This object is for creating new HSPs.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Search::HSP::HSPFactory->new();
Function: Builds a new Bio::Search::HSP::HSPFactory object
Returns : Bio::Search::HSP::HSPFactory
Args :
create
Title : create
Usage : $factory->create(%args)
Function: Create a new L<Bio::Search::HSP::HSPI> object
Returns : L<Bio::Search::HSP::HSPI>
Args : hash of initialization parameters
type
Title : type
Usage : $factory->type('Bio::Search::HSP::GenericHSP');
Function: Get/Set the HSP creation type
Returns : string
Args : [optional] string to set
perl v5.14.2 2012-03-02 Bio::Search::HSP::HSPFactory(3pm)
Check Out this Related Man Page
Bio::Search::HSP::PSLHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::PSLHSP(3pm)NAME
Bio::Search::HSP::PSLHSP - A HSP for PSL output
SYNOPSIS
# get a PSLHSP somehow (SearchIO::psl)
DESCRIPTION
This is a HSP for PSL output so we can handle seq_inds differently.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Search::HSP::PSLHSP->new();
Function: Builds a new Bio::Search::HSP::PSLHSP object
Returns : an instance of Bio::Search::HSP::PSLHSP
Args : -gapblocks => arrayref of gap locations which are [start,length]
of gaps
gap_blocks
Title : gap_blocks
Usage : $obj->gap_blocks($seqtype,$blocks)
Function: Get/Set the gap blocks
Returns : value of gap_blocks (a scalar)
Args : sequence type - 'query' or 'hit'
blocks - arrayref of block start,length
mismatches
Title : mismatches
Usage : $obj->mismatches($newval)
Function: Get/Set the number of mismatches
Returns : value of mismatches (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::Search::HSP::PSLHSP(3pm)