Bio::SeqFeature::SimilarityPair(3pm)			User Contributed Perl Documentation		      Bio::SeqFeature::SimilarityPair(3pm)

NAME

       Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
			 of two sequences.

SYNOPSIS

	 $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);

	 $sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
	 $sim = $sim_pair->hit();   # dto - the hit.

	 # some properties for the similarity pair
	 $expect = $sim_pair->significance();
	 $score = $sim_pair->score();
	 $bitscore = $sim_pair->bits();

	 # this will not write the description for the sequence (only its name)
	 print $sim_pair->query()->gff_string(), "
";

DESCRIPTION

       Lightweight similarity search result as a pair of Similarity features. This class inherits off Bio::SeqFeature::FeaturePair and therefore
       implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, with better support for
       representing similarity search results in a cleaner way.

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 - Hilmar Lapp
       Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com

APPENDIX

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

   new
	Title	: new
	Usage	: my $similarityPair = Bio::SeqFeature::SimilarityPair->new
					(-hit	=> $hit,
					 -query => $query,
					 -source => 'blastp');
	Function: Initializes a new SimilarityPair object
	Returns : Bio::SeqFeature::SimilarityPair
	Args	: -query => The query in a Feature pair
		  -hit	 => (formerly '-subject') the subject/hit in a Feature pair

   query
	Title	: query
	Usage	: $query_feature = $obj->query();
		  $obj->query($query_feature);
	Function: The query object for this similarity pair
	Returns : Bio::SeqFeature::Similarity
	Args	: [optional] Bio::SeqFeature::Similarity

       See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair

   subject
	Title	: subject
	Usage	: $sbjct_feature = $obj->subject();
		  $obj->subject($sbjct_feature);
	Function: Get/Set Subject for a SimilarityPair
	Returns : Bio::SeqFeature::Similarity
	Args	: [optional] Bio::SeqFeature::Similarity
	Notes	: Deprecated.  Use the method 'hit' instead

   hit
	Title	: hit
	Usage	: $sbjct_feature = $obj->hit();
		  $obj->hit($sbjct_feature);
	Function: Get/Set Hit for a SimilarityPair
	Returns : Bio::SeqFeature::Similarity
	Args	: [optional] Bio::SeqFeature::Similarity

   source_tag
	Title	: source_tag
	Usage	: $source = $obj->source_tag(); # i.e., program
		  $obj->source_tag($evalue);
	Function: Gets the source tag (program name typically) for a feature
	Returns : string
	Args	: [optional] string

   significance
	Title	: significance
	Usage	: $evalue = $obj->significance();
		  $obj->significance($evalue);
	Function:
	Returns :
	Args	:

   score
	Title	: score
	Usage	: $score = $obj->score();
		  $obj->score($value);
	Function:
	Returns :
	Args	:

   bits
	Title	: bits
	Usage	: $bits = $obj->bits();
		  $obj->bits($value);
	Function:
	Returns :
	Args	:

perl v5.14.2							    2012-03-02				      Bio::SeqFeature::SimilarityPair(3pm)