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

Bio::Search::GenericDatabase(3pm)			User Contributed Perl Documentation			 Bio::Search::GenericDatabase(3pm)

NAME

       Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI

SYNOPSIS

	   use Bio::Search::GenericDatabase;

	   $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
						    -date => '2001-03-13',
						    -length => 2352511,
						    -entries => 250000 );

	   $name = $db->name();
	   $date = $db->date();
	   $num_letters = $db->letters();
	   $num_entries = $db->entries();

DESCRIPTION

       This module provides a basic implementation of Bio::Search::DatabaseI.  See documentation in that module for more information.

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Steve Chervitz <sac@bioperl.org>

       See the FEEDBACK section  for where to send bug reports and comments.

COPYRIGHT

       Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods.

   name
       See Bio::Search::DatabaseI::name() for documentation

       This implementation is a combined set/get accessor.

   date
       See Bio::Search::DatabaseI::date() for documentation

       This implementation is a combined set/get accessor.

   letters
       See Bio::Search::DatabaseI::letters() for documentation

       This implementation is a combined set/get accessor.

   entries
       See Bio::Search::DatabaseI::entries() for documentation

       This implementation is a combined set/get accessor.

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

Check Out this Related Man Page

Bio::Search::Hit::Fasta(3pm)				User Contributed Perl Documentation			      Bio::Search::Hit::Fasta(3pm)

NAME

       Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits

SYNOPSIS

	 # You wouldn't normally create these manually;
	 # instead they would be produced by Bio::SearchIO::fasta

	 use Bio::Search::Hit::Fasta;
	 my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01);

DESCRIPTION

       Bio::Search::Hit::HitI objects are data structures that contain information about specific hits obtained during a library search.  Some
       information will be algorithm-specific, but others will be generally defined, such as the ability to obtain alignment objects corresponding
       to each hit.

SEE ALSO

       Bio::Search::Hit::HitI, Bio::Search::Hit::GenericHit, Bio::SearchIO::fasta.

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 one of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Aaron Mackey
       Email amackey-at-virginia.edu

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   _initialize
	Function: where the heavy stuff will happen when new is called

   AUTOLOAD
	Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL

perl v5.14.2							    2012-03-02					      Bio::Search::Hit::Fasta(3pm)
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