tfbs::patterni(3pm) [debian man page]
TFBS::PatternI(3pm) User Contributed Perl Documentation TFBS::PatternI(3pm) NAME
TFBS::PatternI - interface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions ) DESCRIPTION
TFBS::PatternI is a draft class that should contain general interface for matrix and other (future) pattern objects. It is not defined and not used yet, as I need to ponder over certain unresolved issues in general pattern definition. User feedback is more than welcome. 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. ID Title : ID Usage : my $ID = $icm->ID() $pfm->ID('M00119'); Function: Get/set on the ID of the pattern (unique in a DB or a set) Returns : pattern ID (a string) Args : none for get, string for set name Title : name Usage : my $name = $pwm->name() $pfm->name('PPARgamma'); Function: Get/set on the name of the pattern Returns : pattern name (a string) Args : none for get, string for set class Title : class Usage : my $class = $pwm->class() $pfm->class('forkhead'); Function: Get/set on the structural class of the pattern Returns : class name (a string) Args : none for get, string for set tag Title : tag Usage : my $acc = $pwm->tag('acc') $pfm->tag(source => "Gibbs"); Function: Get/set on the structural class of the pattern Returns : tag value (a scalar/reference) Args : tag name (string) for get, tag name (string) and value (any scalar/reference) for set all_tags Title : all_tags Usage : my %tag = $pfm->all_tags(); Function: get a hash of all tags for a matrix Returns : a hash of all tag values keyed by tag name Args : none delete_tag Title : delete_tag Usage : $pfm->delete_tag('score'); Function: get a hash of all tags for a matrix Returns : nothing Args : a string (tag name) perl v5.14.2 2008-01-24 TFBS::PatternI(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)