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.IX Title "Bio::DB::GFF::Aggregator::clone 3pm"
.TH Bio::DB::GFF::Aggregator::clone 3pm "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::GFF::Aggregator::clone \-\- Clone aggregator
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::DB::GFF;
\&
\&  # Open the sequence database
\&  my $db      = Bio::DB::GFF\->new( \-adaptor => \*(Aqdbi:mysql\*(Aq,
\&                                   \-dsn     => \*(Aqdbi:mysql:elegans42\*(Aq,
\&                                   \-aggregator => [\*(Aqtranscript\*(Aq,\*(Aqclone\*(Aq],
\&                                 );
\&
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
\& Aggregator method: clone
\& Main method:       \-none\-
\& Sub methods:       Clone_left_end Clone_right_end region:Genomic_canonical
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and
was written to be compatible with the C elegans \s-1GFF\s0 files.  It
aggregates raw \*(L"Clone_left_end\*(R", \*(L"Clone_right_end\*(R", and
\&\*(L"region:Genomic_canonical\*(R" features into composite features of type
\&\*(L"clone\*(R".
.SS "aggregate"
.IX Subsection "aggregate"
.Vb 6
\& Title   : aggregate
\& Usage   : $features = $a\->aggregate($features,$factory)
\& Function: aggregate a feature list into composite features
\& Returns : an array reference containing modified features
\& Args    : see L<Bio::DB::GFF::Aggregator>
\& Status  : Public
.Ve
.PP
The WormBase \s-1GFF\s0 model is unusual in that clones aren't identified as
a single feature with start and stop positions, but as two features, a
\&\*(L"left end\*(R" and a \*(L"right end\*(R".  One or both of these features may be
absent.  In order to accommodate this, the aggregator will return undef
for the start and/or stop if one or both of the ends are missing.
.SS "method"
.IX Subsection "method"
.Vb 6
\& Title   : method
\& Usage   : $aggregator\->method
\& Function: return the method for the composite object
\& Returns : the string "clone"
\& Args    : none
\& Status  : Public
.Ve
.SS "part_names"
.IX Subsection "part_names"
.Vb 6
\& Title   : part_names
\& Usage   : $aggregator\->part_names
\& Function: return the methods for the sub\-parts
\& Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
\& Args    : none
\& Status  : Public
.Ve
.SH "BUGS"
.IX Header "BUGS"
None reported.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, Bio::DB::GFF::Aggregator
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory.
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.