Bio::Phylo::NeXML::Entities - Functions for dealing with XML entities
This package provides subroutines for dealing with characters that need to be encoded as XML entities,
and decoded in other formats.
For example: & needs to be encoded as & in XML.
The subroutines have the same signatures and the same names as those in the commonly-used module HTML::Entities.
They are re-implemented here to avoid introducing dependencies.
The following subroutines are utility functions that can be imported using:
use Bio::Phylo::NeXML::Entities '/entities/';
Encodes problematic characters as XML entities
Type : Utility function
Title : encode_entities
Usage : my $encoded = encode_entities('string with & or >','>&')
Function: Encodes entities in first argument string
Returns : Modified string
Args : Required, first argument: a string to encode
Optional, second argument: a string that specifies
which characters to encode
Decodes XML entities into the characters they code for
Type : Utility function
Title : decode_entities
Usage : my $decoded = decode_entities('string with & or >')
Function: decodes encoded entities in argument string(s)
Returns : Array of decoded strings
Args : One or more encoded strings
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
