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Bio::Biblio::IO::medlinexml(3pm) User Contributed Perl Documentation Bio::Biblio::IO::medlinexml(3pm)

NAME

Bio::Biblio::IO::medlinexml - a converter of XML files with MEDLINE citations

VERSION

version 1.70

SYNOPSIS

Do not use this object directly, it is recommended to access it and use it through the Bio::Biblio::IO module:

  use Bio::Biblio::IO;
  my $io = Bio::Biblio::IO->new(-format => 'medlinexml');

DESCRIPTION

This object reads bibliographic citations in XML/MEDLINE format and converts them into Bio::Biblio::RefI objects. It is an implementation of methods defined in Bio::Biblio::IO.

The main documentation details are to be found in Bio::Biblio::IO.

METHODS

next_bibref

FUNCTIONS

handle_doc_start

handle_doc_end

handle_char

handle_start

handle_end

INTERNAL METHODS

_initialize

_parse

_process_citation

What to do when we have the whole $citation ready

_add_element

Add $element into an array named $key to the top object at @ObjectStack; if $element is empty, take it from @PCDataStack

_data2obj

Remove top of @PCDataStack and put it into top object at @ObjectStack under name $key

_obj2obj

Remove top of @ObjectStack and put it into now-top at @ObjectStack under name $key

_eq_hash_elem

Check if a $key exists in a ref-hash $rh and if it is equal to $value

_debug_object_stack

--- only for debugging

FEEDBACK

Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

LEGAL

Authors

Martin Senger <senger@ebi.ac.uk>

This software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself

2023-02-14 perl v5.36.0