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Bio::DB::Biblio::pdf.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::DB::Biblio::pdf - Fetch PDF for a PubMed IDSYNOPSIS
Do not use this object directly, it is recommended to access it and use it through the Bio::Biblio module:use Bio::Biblio; my $biblio = new Bio::Biblio (-access => 'pdf');
DESCRIPTION
This object contains the real implementation of a Bibliographic Query Service as defined in Bio::DB::BiblioI.Bio::DB::BiblioI is not implemented as documented in the interface, particularly the find() method, which is not compatible with PubMed's query language.
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
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:
http://bugzilla.open-bio.org/
AUTHOR
Allen Day <allenday@ucla.edu>COPYRIGHT
Copyright (c) 2004 Allen Day, University of California, Los Angeles.This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER
This software is provided ``as is'' without warranty of any kind.BUGS AND LIMITATIONS
- •
- Of course, you'll need access to the sites hosting the PDFs to download them.
= item *
If you're having problems retrieving PDF from a site you have access to, you might try adjusting the max_depth() attribute. It is default set to 3, and affects how many links deep will be recursively followed in page fetches to try to find your PDF.
SEE ALSO
Pub Med Help http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html Entrez Utilities http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
APPENDIX
The main documentation details are to be found in Bio::DB::BiblioI.Here is the rest of the object methods. Interface methods first, followed by internal methods.
_initialize
Usage : my $obj = new Bio::Biblio (-access => 'pdf' ...); (_initialize is internally called from this constructor) Returns : 1 on success Args : none
This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object).
Note that this method is called always as an object method (never as a class method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one.
get_next
Title : get_next Usage : $xml = $biblio->get_next(); Function: return next record as xml Returns : an xml string Args : none
find
Title : find Usage : $biblio = $biblio->find(1234); Function: perform a PubMed query by PubMed ID Returns : a reference to the object on which the method was called Args : a PubMed ID
exists
Title : exists Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
destroy
Title : destroy Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
get_vocabulary_names
Title : get_vocabulary_names Usage : do not use Function: no-op. this is here only for interface compatibility Returns : empty arrayref Args : none
contains
Title : contains Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
get_entry_description
Title : get_entry_description Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
get_all_values
Title : get_all_values Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
get_all_entries
Title : get_all_entries Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Internal methods unrelated to Bio::DB::BiblioI
depth()
Usage : $obj->depth($newval) Function: track link recursion depth Example : Returns : value of depth (a scalar) Args : on set, new value (a scalar or undef, optional)
max_depth()
Usage : $obj->max_depth($newval) Function: how far should link recursion go? Example : Returns : value of max_depth (a scalar) Args : on set, new value (a scalar or undef, optional)
ua()
Usage : $obj->ua($newval) Function: holds an LWP::UserAgent instance Example : Returns : value of ua (a scalar) Args : on set, new value (a scalar or undef, optional)
pdf()
Usage : $obj->pdf($newval) Function: holds pdf data Example : Returns : value of pdf (a scalar) Args : on set, new value (a scalar or undef, optional)
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Design ©2006-2024 Maxime Vantorre