NAME

Bio::Tools::WWW.pm - Bioperl manager for web resources related to biology.

SYNOPSIS

Object Creation

use Bio::Tools qw(:obj);

$pdb = $BioWWW->home_url('pdb');

There is no need to create a new Bio::Tools::WWW.pm object when the :obj tag is used. This tag will import the static $BioWWW object created by Bio::Tools::WWW.pm into your name space. This saves you from having to call new Bio::Tools::WWW.

You are free to not use the :obj tag and create the object as you like, but a Bio::Tools::WWW object is not configurable; any given script only needs a single copy.

INSTALLATION

This module is included with the central Bioperl distribution:

http://bio.perl.org/Core/Latest
ftp://bio.perl.org/pub/DIST

You also need to define URLs for the following variables in this package:

$Not_found_url : Generic page to show in place of a 404 error.
$Tmp_url       : Web-accessible site that is Used for scripts that 
                 need to generate temporary, web-accessible files.
                 The files need not necessarily be HTML files, but 
                 being on the same disk as the server will permit 
                 faster IO from server scripts.

DESCRIPTION

Bio::Tools::WWW is primarily a URL broker for a select set of sites related to bioinformatics/genome analysis. It definitely represents a biased, unexhaustive set. It might be more accurate to call this module "Bio::Tools::URL.pm". But this module does handle some non-URL things and it may do more of this in the future. Having one module to cover all biologically relevant web utilities makes it more convenient, especially at this early stage of development.

Maintaining accurate URLs over time can be challenging as new web sites spring up and old sites are re-organized. Because of this fact, the URLs in this module are not guaranteed to be correct or exhaustive and will require periodic updating.

URL Management

By keeping URL management within Bio::Tools::WWW.pm, other generic modules can easily access a variety of different web sites without having to know about a potential multitude of specific modules specialized for one database or another. A specific example of this is in Bio::Tools::Blast.pm where the function blast_to_html() needs access to different URLs in order to add database links to the Blast report. An alternative approach would be to have multiple blast_to_html() functions defined within modules specialized for Blast analyses of different datasets. This, however, may create maintenance headaches when updating the different versions of the function.

Complex Websites

Websites with complex datasets may require special treatment within this module. As an example, URLs for the Saccharomyces Genome Database are clustered separately in this module, due to (1) the different ways to access information at this database and (2) the familiarity of the developer with this database. The Bio::SGD::WWW.pm inherits from Bio::Tools::WWW.pm to permit access to the URLs provided by Bio::Tools::WWW.pm and to SGD-specific HTML and images.

The organization of Bio::Tools::WWW.pm is expected to evolve as websites get born, die, and mutate their APIs.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

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

bioperl-bugs@bio.perl.org                   
http://bio.perl.org/bioperl-bugs/

AUTHOR

Steve A. Chervitz, sac@genome.stanford.edu

VERSION

Bio::Tools::WWW.pm, 0.014

COPYRIGHT

APPENDIX

Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.

home_url

Usage     : $BioWWW->home_url(<string>)
Purpose   : To obtain the homepage URL for a biological database or resource.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments are:
          :    bioperl  bioperl-schema  biomoo  bsm  ebi  emotif  entrez 
          :    expasy  mips  mmdb  ncbi  pir  pfam  pdb  geneQuiz  
          :    molMov  pubmed  sacch3d  sgd  scop  swissProt  webmol  ypd
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : The URLs listed here do not represent a complete list.
          : Expect this to evolve and grow with time.

See Also : search_url()

search_url

Usage     : $BioWWW->search_url(<string>)
Purpose   : To provide a URL stem for a search engine at a biological database 
          : or resource.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments are:
          :   3db  embl  cath  ec1  ec2  ec3  emotif_id  entrez  gb1  gb2  
          :   gb3  gb4  gb5  pdb  medline  mmdb  pdb  pdb_coord  pfam  pir_acc  
          :   pdbSum  molMov  swpr  swModel  swprSearch  scop  scop_pdb  scop_data 
          :   ypd
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : Unlike the homepage URLs, this method does not return a complete
          : URL but a stem which must be further modified, typically by
          : appending data to it, before it can be used. The data appended
          : depends on the specific URL; typically, it is a database ID or
          : other unique identifier.
          : The requirements for each URL will be described here eventually.
          : 
          : The URLs listed here do not represent a complete list.
          : Expect this to evolve and grow with time.
          :
          : Given this complexity, it may be useful to provide special methods
          : for these different URLs. This would however result in an 
          : explosion of methods that might make this module less 
          : maintainable and harder to use.

stem_url

Usage     : $BioWWW->stem_url(<string>)
Purpose   : To obtain the minimal stem URL for searching a biological database or resource.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments are:
          :    emotif  entrez  pdb
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : The URLs stems returned by this method are much more minimal than
          : this provided by search_url(). Use of these stems requires knowledge
          : of the CGI scripts which they invoke.

See Also : search_url()

viewer_url

Usage     : $BioWWW->viewer_url(<string>)
Purpose   : To obtain the stem URL for a 3D viewer (RasMol, WebMol, Cn3D)
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments are:
          :    rasmol webmol cn3d java  (java is an alias for webmol)
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : The 4-letter Brookhaven PDB identifier must be appended to the
          : URL provided by this method.
          : The URLs listed here do not represent a complete list.
          : Expect this to evolve and grow with time.

not_found_url

Usage     : $BioWWW->not_found_url()
Purpose   : To obtain the URL for a web page to be shown in place of a 404 error.
Returns   : String containing the URL (including "http://")
Argument  : n/a
Throws    : n/a
Comments  : This URL should be customized as desired.

tmp_url

Usage     : $BioWWW->tmp_url()
Purpose   : To obtain the URL for a temporary, web-accessible directory.
Returns   : String containing the URL (including "http://")
Argument  : n/a
Throws    : n/a
Comments  : This URL should be customized  as desired.

search_link

Usage     : $BioWWW->search_link(<site>, <value>, <text>)
Purpose   : Wrapper for search_url() that returns the URL within an HTML anchor.
Returns   : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
Argument  : <site>  = string to be used as argument for search_url()
          : <value> = string to be appended to the search URL stem.
          : <text>  = string to be shown as the link text (default = <value>).
Throws    : n/a
Status    : Experimental

See Also : search_url()

viewer_link

Usage     : $BioWWW->viewer_link(<site>, <value>, <text>)
Purpose   : Wrapper for viewer_url() that returns the complete URL within an HTML anchor.
Returns   : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
Argument  : <site>  = string to be used as argument for viewer_url()
          : <value> = string to be appended to the viewer URL stem.
          : <text>  = string to be shown as the link text (default = <value>).
Throws    : n/a
Status    : Experimental

html

Usage     : $BioWWW->html(<string>)
Purpose   : To obtain HTML-formatted text for frequently needed web-page messages.
Returns   : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
Argument  : String.
          : Currently acceptable arguments are:
          :   authority  (mailto: link for webmaster; shows e-mail address as link)
          :   notify     (wraps mailto:authority link with text for link "please notify us")
          :   ourFault   ("this problem is our fault. If it persists <notify-link>")
          :   trouble    (same as ourFault but doesn't blame us for the problem)
          :   techDiff   ("we are experiencing technical difficulties. Please stand by.")
Throws    : n/a
Comments  : The authority (webmaster) is imported from the Bio::Root::Global.pm
          : module. The value for $AUTHORITY should be set there, or
          : customize this module so that it doesn't use Bio::Root::Global.pm.

sgd_url

Usage     : $BioWWW->sgd_url(<string>)
Purpose   : To obtain the webpage URL or search stem for SGD.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments (TODO).
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : This accessor is specialized for the Saccharomyces Genome Database.
          : It is possible that it will be moved to SGD::WWW.pm in the future.

See Also : search_url()

s3d_url

Usage     : $BioWWW->s3d_url(<string>)
Purpose   : To obtain the webpage URL or search stem for Sacch3D.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments (TODO).
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : This accessor is specialized for the Saccharomyces Genome Database.
          : It is possible that it will be moved to SGD::WWW.pm in the future.

See Also : search_url()

sgd_stem_url

Usage     : $BioWWW->sgd_stem_url(<string>)
Purpose   : To obtain the minimal stem URL for a SGD/Sacch3D CGI script.
Returns   : String containing the URL (including "http://")
Argument  : String
          : Currently acceptable arguments (TODO).
Throws    : Warns if argument cannot be resolved to a URL.
Comments  : This accessor is specialized for the Saccharomyces Genome Database.
          : It is possible that it will be moved to SGD::WWW.pm in the future.

See Also : search_url()

s3d_link

Usage     : $BioWWW->s3d_link(<site>, <value>, <text>)
Purpose   : Wrapper for s3d_url() that returns the complete URL within an HTML anchor.
Returns   : String containing the URL (including "http://")
Argument  : <site>  = string to be used as argument for s3d_url()
          : <value> = string to be appended to the s3d URL stem.
          : <text>  = string to be shown as the link text (default = <value>).
Throws    : n/a
Status    : Experimental
Comments  : This accessor is specialized for the Saccharomyces Genome Database.
          : It is possible that it will be moved to SGD::WWW.pm in the future.

sgd_link

Usage     : $BioWWW->sgd_link(<site>, <value>, <text>)
Purpose   : Wrapper for sgd_url() that returns the complete URL within an HTML anchor.
Returns   : String containing the URL (including "http://")
Argument  : <site>  = string to be used as argument for sgd_url()
          : <value> = string to be appended to the sgd URL stem.
          : <text>  = string to be shown as the link text (default = <value>).
Throws    : n/a
Status    : Experimental
Comments  : This accessor is specialized for the Saccharomyces Genome Database.
          : It is possible that it will be moved to SGD::WWW.pm in the future.

start_html

Usage     : $BioWWW->start_html()
Purpose   : Prints the "Content-type: text/html\n\n<HTML>\n" header.
Returns   : n/a; This method prints the Content-type string shown above.
Argument  : n/a
Throws    : n/a
Status    : Experimental
Comments  : This method prevents redundant invocations thus avoiding th
          : accidental printing of the "content-type..." on the page.
          : If using L. Stein's CGI.pm, this is similar to $query->header()
          : (Does CGI.pm prevent redundant invocation?)

redirect

Usage     : $BioWWW->redirect(<string>)
Purpose   : Prints the header needed to redirect a web browser to a supplied URL. 
Returns   : n/a; Prints the redirection header.
Argument  : String containing the URL to be redirected to.
Throws    : n/a
Status    : Experimental

pre

Usage     : $BioWWW->pre("text to be pre-formatted");
Purpose   : To produce HTML for text that is not to be formated by the brower.
Returns   : String containing the "<pre>" formatted html.
Argument  : n/a
Throws    : n/a
Status    : Experimental

strip_html

Usage     : $boolean = &strip_html( string_ref, [fast] );
Purpose   : Removes HTML formatting from a supplied string.
Returns   : Boolean: true if string was stripped, false if not.
Argument  : string_ref = reference to a string containing the whole 
          :              web page to be stripped.
          : fast = a non-zero value. Optional. If set, a faster 
          :        but perhaps less thorough procedure is used for
          :        stripping. Default = not fast.
Throws    : Exception if the argument is not a scalar reference.
Comments  : Based on code originally written by Alex Dong Li
          : (ali@genet.sickkids.on.ca).
          : This is a more generic version of the function that appears 
          : in Bio::Tools::Blast::HTML.pm
          : This version does not perform any Blast-specific stripping.
          :
          : This employs a simple method for removing tags that
          : will fail under following conditions:
          :  1) if quoted > appears in a tag  (does this ever happen?)
          :  2) if a tag is split over multiple lines and this method is
          :     used to process one line at a time.
          :
          : Without fast mode, large HTML files can take exceedingly long times to
          : strip (e.g., 1Meg file with many tags can take 10 minutes versus 5 seconds
          : in fast mode. Try the swissprot yeast table). If you know the HTML to be
          : well-behaved (i.e., tags are not split across mutiple lines), use fast
          : mode for large, dense files.

FOR DEVELOPERS ONLY

Data Members

An instance of Bio::Tools::WWW.pm is a blessed reference to a hash containing all or some of the following fields:

FIELD           VALUE
--------------------------------------------------------------
_started_html   Defined the on the initial invocation of start_html()
                to avoid duplicate printing out the "Content-type..." header.

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

SYNOPSIS

Object Creation

INSTALLATION

DESCRIPTION

URL Management

Complex Websites

SEE ALSO

FEEDBACK

Mailing Lists

Reporting Bugs

AUTHOR

VERSION

COPYRIGHT

APPENDIX

home_url

search_url

stem_url

viewer_url

not_found_url

tmp_url

search_link

viewer_link

html

sgd_url

s3d_url

sgd_stem_url

s3d_link

sgd_link

start_html

redirect

pre

strip_html

FOR DEVELOPERS ONLY

Data Members

Module Install Instructions