Bio::Search::Hit::HitI - Abstract interface for Hit objects
This is a abstract class meant to define an interface, and nothing more.
Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_hit_id Usage : $id = $hit->get_hit_id(); Function: Used to obtain the id of the matched entity. Returns : a scalar string Args : <none>
Title : get_hit_desc Usage : $desc = $hit->get_hit_desc(); Function: Used to obtain the description of a matched entity Returns : a scalar string Args : <none>
Title : get_algorithm Usage : $which = $hit->get_algorithm(); Function: Used to obtain the algorithm specification used to obtain the hit Returns : a scalar string Args : <none>
Title : get_raw_score Usage : $score = $hit->get_raw_score(); Function: Used to obtain the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : <none>
Title : get_expectation_value Usage : $evalue = $hit->get_expectation_value(); Function: Used to obtain the E() value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : <none>
Title : get_evalue Usage : $evalue = $hit->get_evalue(); Function: same as get_expectation_value (just an alias) Returns : see above Args : <none>
Title : get_alignments Usage : @aligns = $hit->get_alignments() Function: Used to obtain an array of Bio::Alignment objects corresponding to the Hit. Returns : an array of Alignment objects, if more than one Alignments exist and called in wantarray context. In scalar context will return a reference to an array of Alignment objects, if more than one Alignment objects exist, otherwise will return the unique Alignment object. If no Alignment objects exist, returns undef Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.