bio::search::databasei(3pm) [debian man page]
Bio::Search::DatabaseI(3pm) User Contributed Perl Documentation Bio::Search::DatabaseI(3pm) NAME
Bio::Search::DatabaseI - Interface for a database used in a sequence search SYNOPSIS
Bio::Search::DatabaseI objects should not be instantiated since this module defines a pure interface. Given an object that implements the Bio::Search::DatabaseI interface, you can do the following things with it: $name = $db->name(); $date = $db->date(); $num_letters = $db->letters(); $num_entries = $db->entries(); DESCRIPTION
This module defines methods for an object that provides metadata information about a database used for sequence searching. 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 Usage : $name = $db->name(); Purpose : Get the name of the database searched. Returns : String Argument : n/a date Usage : $date = $db->date(); Purpose : Get the creation date of the queried database. Returns : String Argument : n/a letters Usage : $num_letters = $db->letters(); Purpose : Get the number of letters in the queried database. Returns : Integer Argument : n/a entries Usage : $num_entries = $db->entries(); Purpose : Get the number of entries in the queried database. Returns : Integer Argument : n/a perl v5.14.2 2012-03-02 Bio::Search::DatabaseI(3pm)
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Bio::Search::Result::WABAResult(3pm) User Contributed Perl Documentation Bio::Search::Result::WABAResult(3pm) NAME
Bio::Search::Result::WABAResult - Result object for WABA alignment output SYNOPSIS
# use this object exactly as you would a GenericResult # the only extra method is query_database which is the # name of the file where the query sequence came from DESCRIPTION
This object is for WABA result output, there is little difference between this object and a GenericResult save the addition of one method query_database. Expect many of the fields for GenericResult to be empty however as WABA was not intended to provide a lot of extra information other than the alignment. 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::Result::WABAResult->new(); Function: Builds a new Bio::Search::Result::WABAResult object Returns : Bio::Search::Result::WABAResult Args : -query_database => "name of the database where the query came from" query_database Title : query_database Usage : $obj->query_database($newval) Function: Data field for the database filename where the query sequence came from Returns : value of query_database Args : newvalue (optional) All other methods are inherited from Bio::Search::Result::GenericResult See the Bio::Search::Result::GenericResult for complete documentation of the rest of the methods that are available for this module. perl v5.14.2 2012-03-02 Bio::Search::Result::WABAResult(3pm)