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.IX Title "TFBS::PatternI 3pm"
.TH TFBS::PatternI 3pm 2024-03-13 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH NAME
TFBS::PatternI \- interface definition for all pattern objects (currently
includes matrices and word (consensus and regular expressions )
.SH DESCRIPTION
.IX Header "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.
.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 ID
.IX Subsection "ID"
.Vb 6
\& Title   : ID
\& Usage   : my $ID = $icm\->ID()
\&           $pfm\->ID(\*(AqM00119\*(Aq);
\& 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
.Ve
.SS name
.IX Subsection "name"
.Vb 6
\& Title   : name
\& Usage   : my $name = $pwm\->name()
\&           $pfm\->name(\*(AqPPARgamma\*(Aq);
\& Function: Get/set on the name of the pattern
\& Returns : pattern name (a string)
\& Args    : none for get, string for set
.Ve
.SS class
.IX Subsection "class"
.Vb 6
\& Title   : class
\& Usage   : my $class = $pwm\->class()
\&           $pfm\->class(\*(Aqforkhead\*(Aq);
\& Function: Get/set on the structural class of the pattern
\& Returns : class name (a string)
\& Args    : none for get, string for set
.Ve
.SS tag
.IX Subsection "tag"
.Vb 7
\& Title   : tag
\& Usage   : my $acc = $pwm\->tag(\*(Aqacc\*(Aq)
\&           $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
.Ve
.SS all_tags
.IX Subsection "all_tags"
.Vb 5
\& 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
.Ve
.SS delete_tag
.IX Subsection "delete_tag"
.Vb 5
\& Title   : delete_tag
\& Usage   : $pfm\->delete_tag(\*(Aqscore\*(Aq);
\& Function: get a hash of all tags for a matrix
\& Returns : nothing
\& Args    : a string (tag name)
.Ve