Provided by: libbio-perl-perl_1.7.6-3_all bug


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


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


       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.


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

        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

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

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

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

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

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

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

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

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