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)
Check Out this Related 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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