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The Lounge What is on Your Mind? Announcement: New Discourse Site to Go Live this Weekend Post 303045446 by Neo on Tuesday 24th of March 2020 01:43:37 AM
Old 03-24-2020
Update:

The moderation team has decided to open both forums, the old vB forum (this one) and the new one (Discourse forum) for the time being.

We want to get more user feedback and also consider fixing some small nits related to how code is preprocessed on the discourse side, from here.

Scrutinizer did an excellent check and notice that the preprocessing of the code in posts turned \n in code fragments to hard new lines in the results on discourse.

We are looking into the best was to fix this.
This User Gave Thanks to Neo For This Post:
 
Test Your Knowledge in Computers #276
Difficulty: Easy
OpenSolaris was based on Solaris, which was originally released by Sun in 1999.
True or False?

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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)

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