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bio::search::hsp::wabahsp(3pm) [debian man page]

Bio::Search::HSP::WABAHSP(3pm)				User Contributed Perl Documentation			    Bio::Search::HSP::WABAHSP(3pm)

NAME

       Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

SYNOPSIS

       # use this object as you would a GenericHSP # a few other methods have been added including state

DESCRIPTION

       This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA
       alignment.  We also must implement a method to calculate homology_string since it is not returned by the algorithm in the machine readable
       format.

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@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::WABAHSP->new();
	Function: Builds a new Bio::Search::HSP::WABAHSP object
	Returns : Bio::Search::HSP::WABAHSP
	Args	: -hmmstate_seq => the string representing the state output from WABA

   hmmstate_string
	Title	: hmmstate_string
	Usage	: my $hmmseq = $wabahsp->hmmstate_string();
	Function: Get/Set the WABA HMM stateseq
	Returns : string
	Args	: [optional] string

   homology_string
	Title	: homolgy_string
	Usage	: my $homology_str = $hsp->homology_string();
	Function: Homology string must be calculated for a WABA HSP so we can do
		  so here and cache the result so it is only done once
	Returns : string
	Args	: none

perl v5.14.2							    2012-03-02					    Bio::Search::HSP::WABAHSP(3pm)

Check Out this Related 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)
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