NAME

Bio::Phylo::Adaptor::Bioperl::Datum - Adaptor class for bioperl compatibility

SYNOPSIS

 use Bio::Phylo::Matrices::Datum;
 use Bio::Phylo::Adaptor;

 my $datum = Bio::Phylo::Matrices::Datum->new;

 $Bio::Phylo::COMPAT = 'Bioperl';

 my $seq = Bio::Phylo::Adaptor->new($datum);

 print "compatible!" if $seq->isa('Bio::LocatableSeq');

DESCRIPTION

This class wraps Bio::Phylo datum objects to give them an interface compatible with bioperl.

METHODS

alphabet()

 Title   : alphabet
 Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
 Function: Returns the alphabet of sequence, one of
           'dna', 'rna' or 'protein'. This is case sensitive.

           This is not called <type> because this would cause
           upgrade problems from the 0.5 and earlier Seq objects.

 Returns : a string either 'dna','rna','protein'. NB - the object must
           make a call of the type - if there is no alphabet specified it
           has to guess.
 Args    : none

get_nse()

 Title   : get_nse
 Usage   :
 Function: read-only name of form id/start-end
 Example :
 Returns :
 Args    :

seq()

 Title   : seq()
 Usage   : $string    = $obj->seq()
 Function: Returns the sequence as a string of letters. The
           case of the letters is left up to the implementer.
           Suggested cases are upper case for proteins and lower case for
           DNA sequence (IUPAC standard), but you should not rely on this.
 Returns : A scalar
 Args    : Optionally on set the new value (a string). An optional second
           argument presets the alphabet (otherwise it will be guessed).
           Both parameters may also be given in named paramater style
           with -seq and -alphabet being the names.

SEE ALSO

Bio::LocatableSeq

Bio::Phylo::Adaptor::Bioperl::Datum is an adaptor that makes Bio::Phylo character data sequences compatible with Bio::LocatableSeq objects.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Datum.pm 4162 2007-07-11 01:35:39Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.