/ 
bioperl-0.7.0
/ Bio::SeqFeature::SimilarityPair

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
$sim = $sim_pair->subject(); # dto.

# 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://bio.perl.org/MailList.html  - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Hilmar Lapp

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

Describe contact details here

APPENDIX

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

from_searchResult

Title   : from_searchResult
Usage   : $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blast_obj);
          $sim_pair->from_searchResult($blast_obj);
Function: This method creates or fills SimilarityPair objects from objects
          representing similarity search results.

          Since there is no public interface search result objects are
          required to implement, this method basically checks for the type
          of the object and dispatches the actual SimilarityPair creation
          to a method capable of this.

          At present, the following classes are recognized:
          Bio::Tools::Blast::Sbjct
          Bio::Tools::Blast::HSP
          An exception will be thrown if an object of an unrecognized class
          is passed.

          Note that this is probably the point where you will want to add
          your class if you have a method for creating SimilarityPair
          objects from it.

          Note that passing an object that has already previously been
          filled is potentially error-prone, because undefined fields
          will not be (re-)set to an undef value.

Returns : The object created or filled.
Args    :

_from_blastObject

Title   : from_blastObject
Usage   : $sim_pair = Bio::SeqFeature::SimilarityPair->_from_blastObj($blast_obj);
          $sim_pair->_from_blastObj($blast_obj);
Function: See documentation for from_searchResult(). This one handles
          Bio::Tools::Blast::Sbjct and Bio::Tools::Blast::HSP objects.
Returns : A SimilarityPair object.
Args    :

query

Title   : query
Usage   : $query_feature = $obj->query();
          $obj->query($query_feature);
Function: 
Returns : 
Args    :

subject

Title   : subject
Usage   : $sbjct_feature = $obj->subject();
          $obj->subject($sbjct_feature);
Function: 
Returns : 
Args    :

source_tag

Title   : source_tag
Usage   : $source = $obj->source_tag(); # i.e., program
          $obj->source_tag($evalue);
Function: 
Returns : 
Args    :

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    :