bio::search::hsp::fastahsp(3pm) [debian man page]
Bio::Search::HSP::FastaHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::FastaHSP(3pm) NAME
Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data SYNOPSIS
# get a FastaHSP from a SearchIO stream my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta'); while( my $r = $in->next_result) { while( my $hit = $r->next_result ) { while( my $hsp = $hit->next_hsp ) { print "smith-waterman score (if available): ", $hsp->sw_score()," "; } } } DESCRIPTION
Describe the object here 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::FastaHSP->new(); Function: Builds a new Bio::Search::HSP::FastaHSP object Returns : Bio::Search::HSP::FastaHSP Args : -swscore => smith-waterman score sw_score Title : sw_score Usage : $obj->sw_score($newval) Function: Get/Set Smith-Waterman score Returns : value of sw_score Args : newvalue (optional) evalue2 Title : evalue2 Usage : $obj->evalue2($newval) Function: Get/Set E2() expectation value Returns : value of evalue2 Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::Search::HSP::FastaHSP(3pm)
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Bio::Search::Hit::HitFactory(3pm) User Contributed Perl Documentation Bio::Search::Hit::HitFactory(3pm) NAME
Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects SYNOPSIS
use Bio::Search::Hit::HitFactory; my $factory = Bio::Search::Hit::HitFactory->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 Hits. 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::Hit::HitFactory->new(); Function: Builds a new Bio::Search::Hit::HitFactory object Returns : Bio::Search::Hit::HitFactory Args : create Title : create Usage : $factory->create(%args) Function: Create a new L<Bio::Search::Hit::HitI> object Returns : L<Bio::Search::Hit::HitI> Args : hash of initialization parameters type Title : type Usage : $factory->type('Bio::Search::Hit::GenericHit'); Function: Get/Set the Hit creation type Returns : string Args : [optional] string to set perl v5.14.2 2012-03-02 Bio::Search::Hit::HitFactory(3pm)