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.\" ========================================================================
.\"
.IX Title "TFBS::SitePairSet 3pm"
.TH TFBS::SitePairSet 3pm "2008-01-24" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::SitePairSet \- a set of TFBS::SitePair objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    my $site_pair_set = TFBS::SitePairSet\->new(@list_of_site_pair_objects);
\&
\&    # add a TFBS::SitePair object to set:
\&    
\&    $site_pair_set\->add_site_pair($site_pair_obj);
\&
\&    # append another TFBS::SitePairSet contents: 
\&
\&    $site_pair_set\->add_site_pair_set($site_pair_obj);
\&
\&    # create an iterator:
\&
\&    my $it = $site_pair_set\->Iterator(\-sort_by => \*(Aqstart\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::SitePairSet is an aggregate class that contains a collection
of TFBS::SitePair objects. It can be created anew and filled with 
TFBS::Site::Pair object. It is also returned by \fIsearch_aln()\fR method call 
of TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "size"
.IX Subsection "size"
.Vb 5
\& Title   : size
\& Usage   : my $size = $sitepairset\->size()
\& Function: returns a number of TFBS::SitePair objects contained in the set
\& Returns : a scalar (integer) 
\& Args    : none
.Ve
.SS "add_site_pair"
.IX Subsection "add_site_pair"
.Vb 6
\& Title   : add_site_pair
\& Usage   : $sitepairset\->add_site_pair($site_pair_object)
\&           $sitepairset\->add_site_pair(@list_of_site_pair_objects)
\& Function: adds TFBS::SitePair objects to an existing TFBS::SitePairSet object
\& Returns : $sitepairset object (usually ignored)
\& Args    : A list of TFBS::SitePair objects to add
.Ve
.SS "add_site_pair_set"
.IX Subsection "add_site_pair_set"
.Vb 8
\& Title   : add_site_pair_set
\& Usage   : $sitepairset\->add_site_pair_set($site_pair_set_object)
\&           $sitepairset\->add_site_pair(@list_of_site_pair_set_objects)
\& Function: adds the contents of other TFBS::SitePairSet objects 
\&           to an existing TFBS::SitePairSet object
\& Returns : $sitepairset object (usually ignored)
\& Args    : A list of TFBS::SitePairSet objects whose contents should be 
\&           added to $sitepairset
.Ve
.SS "Iterator"
.IX Subsection "Iterator"
.Vb 10
\&  Title   : Iterator
\&  Usage   : my $it = $sitepairset\->Iterator(\-sort_by=>\*(Aqstart\*(Aq);
\&            while (my $site_pair = $it\->next()) { #... 
\&  Function: Returns an iterator object, used to iterate thorugh elements 
\&            (TFBS::SitePair objects)
\&  Returns : a TFBS::_Iterator object
\&  Args    : \-sort_by # optional \- currently it accepts 
\&                    #   (default sort order in parenthetse)
\&                    #    \*(Aqname\*(Aq (pattern name, alphabetically)
\&                    #    \*(AqID\*(Aq (pattern/matrix ID, alphabetically)
\&                    #    \*(Aqstart\*(Aq (site start in sequence, 
\&                    #             numerically,increasing order)
\&                    #    \*(Aqend\*(Aq (site end in sequence, 
\&                    #           numerically, increasing order)
\&                    #    \*(Aqscore\*(Aq (1st site in pair,
\&                    #             numerically, decreasing order)
\&            \-reverse # optional \- reverses the default sorting order if true
.Ve
.SS "set1"
.IX Subsection "set1"
.SS "set2"
.IX Subsection "set2"
.Vb 7
\&  Title   : set1
\&            set2
\&  Usage   : my $siteset1 = $sitepairset\->set1();
\&          : my $siteset2 = $sitepairset\->set2()
\&  Function: Returns individual TFBS::SiteSet objects, from the site set pair
\&  Returns : A TFBS::SiteSet object
\&  Args    : none
.Ve
.SS "\s-1GFF\s0"
.IX Subsection "GFF"
.Vb 6
\& Title   : GFF
\& Usage   : print $site\->GFF();
\&         : print $site\->GFF($gff_formatter)
\& Function: returns a "standard" multiline GFF string 
\& Returns : a string (multiline, newline terminated)
\& Args    : a $gff_formatter function reference (optional)
.Ve