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bio::search::hit::hmmer3hit(3pm) [debian man page]

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)

Check Out this Related 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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