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(), "\n";

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    :