TFBS::Word(3pm) User Contributed Perl Documentation TFBS::Word(3pm)NAME
TFBS::Word - base class for word-based patterns
DESCRIPTION
TFBS::Word is a base class consisting of universal constructor called by its subclasses (TFBS::Matrix::*), and word pattern manipulation
methods that are independent of the word type. It is not meant to be instantiated itself.
FEEDBACK
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.
new
word
validate_word
Required in all subclasses
length
search_seq
search_aln
perl v5.14.2 2008-01-24 TFBS::Word(3pm)
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TFBS::SiteSet(3pm) User Contributed Perl Documentation TFBS::SiteSet(3pm)NAME
TFBS::SiteSet - a set of TFBS::Site objects
SYNOPSIS
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 => 'start');
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 search_seq() method call of some TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM).
FEEDBACK
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.
add_site
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
add_site_set
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
size
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
Iterator
Title : Iterator
Usage : my $siteset_iterator =
$siteset->Iterator(-sort_by =>'start');
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 'next' method)
Args : -sort_by # optional - currently it accepts
# (default sort order in parenthetse)
# 'name' (pattern name, alphabetically)
# 'ID' (pattern/matrix ID, alphabetically)
# 'start' (site start in sequence,
# numerically,increasing order)
# 'end' (site end in sequence,
# numerically, increasing order)
# 'score' (numerically, decreasing order)
-reverse # optional - reverses the default sorting order if true
GFF
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)
perl v5.14.2 2008-01-24 TFBS::SiteSet(3pm)