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Rutger Vos
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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