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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::hmmer3Hit(3pm)			User Contributed Perl Documentation			  Bio::Search::Hit::hmmer3Hit(3pm)

NAME
Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object SYNOPSIS
Give standard usage here 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 - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here CONTRIBUTORS
Additional contributors names and emails here 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::HMMERHit->new(); Function: Builds a new Bio::Search::Hit::HMMERHit object Returns : Bio::Search::Hit::HMMERHit Args : Plus the Bio::Search::Hit::GenericHit inherited params -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. next_domain Title : next_domain Usage : my $domain = $hit->next_domain(); Function: An alias for L<next_hsp()>, this will return the next HSP Returns : L<Bio::Search::HSP::HSPI> object Args : none domains Title : domains Usage : my @domains = $hit->domains(); Function: An alias for L<hsps()>, this will return the full list of hsps Returns : array of L<Bio::Search::HSP::HSPI> objects Args : none bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a See Also : score() iteration Title : iteration Usage : $obj->iteration($newval) Function: PSI-BLAST iteration Returns : value of iteration Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::Search::Hit::hmmer3Hit(3pm)
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