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.\" ========================================================================
.\"
.IX Title "TFBS::SiteSet 3"
.TH TFBS::SiteSet 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
TFBS::SiteSet \- a set of TFBS::Site objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    my $site_set = TFBS::SiteSet\->new(@list_of_site_objects);
\&
\&    # add a TFBS::Site object to set:
\&    
\&    $site_set\->add_site($site_obj);
\&
\&    # append another TFBS::SiteSet contents: 
\&
\&    $site_pair_set\->add_site_set($site_obj);
\&
\&    # create an iterator:
\&
\&    my $it = $site_set\->Iterator(\-sort_by => \*(Aqstart\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::SiteSet is an aggregate class that contains a collection
of TFBS::Site objects. It can be created anew and filled with 
TFBS::Site object. It is also returned by \fIsearch_seq()\fR method call 
of some 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 "add_site"
.IX Subsection "add_site"
.Vb 6
\& Title   : add_site
\& Usage   : $siteset\->add_site($site_object)
\&           $siteset\->add_site(@list_of_site_objects)
\& Function: adds TFBS::Site objects to an existing TFBS::SiteSet object
\& Returns : $sitepair object (usually ignored)
\& Args    : A list of TFBS::Site objects to add
.Ve
.SS "add_site_set"
.IX Subsection "add_site_set"
.Vb 8
\& Title   : add_site_set
\& Usage   : $siteset\->add_site_set($site_set_object)
\&           $siteset\->add_site(@list_of_site_set_objects)
\& Function: adds the contents of other TFBS::SiteSet objects 
\&           to an existing TFBS::SiteSet object
\& Returns : $siteset object (usually ignored)
\& Args    : A list of TFBS::SiteSet objects whose contents should be 
\&           added to $siteset
.Ve
.SS "size"
.IX Subsection "size"
.Vb 5
\& Title   : size
\& Usage   : my $size = $siteset\->size()
\& Function: returns a number of TFBS::Site objects contained in the set
\& Returns : a scalar (integer) 
\& Args    : none
.Ve
.SS "Iterator"
.IX Subsection "Iterator"
.Vb 10
\& Title   : Iterator
\& Usage   : my $siteset_iterator = 
\&                   $siteset\->Iterator(\-sort_by =>\*(Aqstart\*(Aq);
\&           while (my $site = $siteset_iterator\->next) {
\&               # do whatever you want with individual matrix objects
\&           }
\& Function: Returns an iterator object that can be used to go through
\&           all members of the set (TFBS::Site objects)
\& Returns : an iterator object (currently undocumentened in TFBS \-
\&                               but understands the \*(Aqnext\*(Aq method)
\& 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 (numerically, decreasing order)
\&                    
\&           \-reverse # optional \- reverses the default sorting order if true
.Ve
.SS "\s-1GFF\s0"
.IX Subsection "GFF"
.Vb 6
\& Title   : GFF
\& Usage   : print $siteset\->GFF();
\&         : print $siteset\->GFF($gff_formatter)
\& Function: returns a "standard" multiline GFF string 
\& Returns : a string (multiline, newline terminated)
\& Args    : a $gff_formatter function reference (optional)
.Ve