Mercurial > repos > mahtabm > ensemb_rep_gvl

comparison variant_effect_predictor/Bio/Tools/WWW.pm @ 0:2bc9b66ada89 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mahtabm
date Thu, 11 Apr 2013 06:29:17 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:2bc9b66ada89
1 #-----------------------------------------------------------------------------
2 # PACKAGE : Bio::Tools::WWW
3 # PURPOSE : To encapsulate commonly used URLs for web key websites in bioinformatics.
4 # AUTHOR : Steve Chervitz
5 # CREATED : 27 Aug 1996
6 # REVISION: $Id: WWW.pm,v 1.12 2002/10/22 07:38:46 lapp Exp $
7 #
8 # For documentation, run this module through pod2html
9 # (preferably from Perl v5.004 or better).
10 #
11 # MODIFIED:
12 # 0.014, sac --- Mon Aug 31 19:41:44 1998
13 # * Updated and added a few URLs.
14 # * Added method strip_html().
15 # * Documentation changes.
16 #
17 #-----------------------------------------------------------------------------
18
19 package Bio::Tools::WWW;
20 use strict;
21 use Bio::Root::Root;
22 use Exporter ();
23 use vars qw(@ISA @EXPORT_OK %EXPORT_TAGS $ID $VERSION $BioWWW $Revision
24 $AUTHORITY);
25 $AUTHORITY = 'nobody@localhost';
26 @ISA = qw( Bio::Root::Root Exporter);
27 @EXPORT_OK = qw($BioWWW);
28 %EXPORT_TAGS = ( obj => [qw($BioWWW)],
29 std => [qw($BioWWW)]);
30
31 $ID = 'Bio::Tools::WWW';
32 $VERSION = 0.014;
33 $Revision = '$Id: WWW.pm,v 1.12 2002/10/22 07:38:46 lapp Exp $'; #'
34
35 ## Static object.
36 $BioWWW = {};
37 bless $BioWWW, $ID;
38 $BioWWW->{'_name'} = "Static $ID object";
39
40
41 ## POD Documentation:
42
43 =head1 NAME
44
45 Bio::Tools::WWW - Bioperl manager for web resources related to biology.
46
47 =head1 SYNOPSIS
48
49 =head2 Object Creation
50
51 use Bio::Tools qw(:obj);
52
53 $pdb = $BioWWW->home_url('pdb');
54
55 There is no need to create a new Bio::Tools::WWW.pm object when the
56 C<:obj> tag is used. This tag will import the static $BioWWW object
57 created by Bio::Tools::WWW.pm into your name space. This saves you
58 from having to call C<new Bio::Tools::WWW>.
59
60 You are free to not use the :obj tag and create the object as you
61 like, but a Bio::Tools::WWW object is not configurable; any given
62 script only needs a single copy.
63
64 =head1 INSTALLATION
65
66 This module is included with the central Bioperl distribution:
67
68 http://bio.perl.org/Core/Latest
69 ftp://bio.perl.org/pub/DIST
70
71 You also need to define URLs for the following variables in this package:
72
73 $Not_found_url : Generic page to show in place of a 404 error.
74 $Tmp_url : Web-accessible site that is Used for scripts that
75 need to generate temporary, web-accessible files.
76 The files need not necessarily be HTML files, but
77 being on the same disk as the server will permit
78 faster IO from server scripts.
79
80 =head1 DESCRIPTION
81
82 Bio::Tools::WWW is primarily a URL broker for a select set
83 of sites related to bioinformatics/genome analysis. It
84 definitely represents a biased, unexhaustive set.
85 It might be more accurate to call this module
86 "Bio::Tools::URL.pm". But this module does handle some non-URL
87 things and it may do more of this in the future. Having one
88 module to cover all biologically relevant web utilities
89 makes it more convenient, especially at this early stage
90 of development.
91
92 Maintaining accurate URLs over time can be challenging as
93 new web sites spring up and old sites are re-organized. Because
94 of this fact, the URLs in this module are not guaranteed to be
95 correct or exhaustive and will require periodic updating.
96
97 =head2 URL Management
98
99 By keeping URL management within Bio::Tools::WWW.pm, other generic
100 modules can easily access a variety of different web sites without
101 having to know about a potential multitude of specific modules
102 specialized for one database or another. An alternative approach would
103 be to have addresses defined within modules specialized for different
104 web sites. This, however, may create maintenance headaches when updating
105 these addresses.
106
107 =head2 Complex Websites
108
109 Websites with complex datasets may require special treatment
110 within this module. As an example,
111 URLs for the Saccharomyces Genome Database are clustered
112 separately in this module, due to (1) the different ways to
113 access information at this database and (2) the familiarity
114 of the developer with this database. The Bio::SGD::WWW.pm inherits from
115 Bio::Tools::WWW.pm to permit access to the URLs provided by Bio::Tools::WWW.pm
116 and to SGD-specific HTML and images.
117
118 The organization of Bio::Tools::WWW.pm is expected to evolve as
119 websites get born, die, and mutate their APIs.
120
121 =head1 SEE ALSO
122
123 http://bio.perl.org/Projects/modules.html - Online module documentation
124 http://bio.perl.org/ - Bioperl Project Homepage
125
126 =head1 FEEDBACK
127
128 =head2 Mailing Lists
129
130 User feedback is an integral part of the evolution of this and other Bioperl modules.
131 Send your comments and suggestions preferably to one of the Bioperl mailing lists.
132 Your participation is much appreciated.
133
134 bioperl-l@bioperl.org - General discussion
135 http://www.bioperl.org/MailList.shtml - About the mailing lists
136
137 =head2 Reporting Bugs
138
139 Report bugs to the Bioperl bug tracking system to help us keep track the bugs and
140 their resolution. Bug reports can be submitted via email or the web:
141
142 bioperl-bugs@bio.perl.org
143 http://bugzilla.bioperl.org/
144
145 =head1 AUTHOR
146
147 Steve Chervitz, sac@bioperl.org
148
149 =head1 VERSION
150
151 Bio::Tools::WWW.pm, 0.014
152
153 =head1 COPYRIGHT
154
155 Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved.
156 This module is free software; you can redistribute it and/or
157 modify it under the same terms as Perl itself.
158
159
160 =cut
161
162
163 #
164 ##
165 ###
166 #### END of main POD documentation.
167 ###
168 ##
169 #
170
171
172 ############################ DATA ##################################
173
174 ### Database homepage links.
175 my %Home_url =
176 (
177 'bioperl' =>'http://bio.perl.org/',
178 'bioperl-stanford'=>'http://genome-www.stanford.edu/perlOOP/bioperl/',
179 'bioperl-schema' =>'http://bio.perl.org/Projects/Schema/',
180 'biomoo' =>'http://bioinformatics.weizmann.ac.il/BioMOO/',
181 'blast_ncbi' =>'http://www.ncbi.nlm.nih.gov/BLAST/',
182 'blast_wu' =>'http://blast.wustl.edu/',
183 'bsm' =>'http://www.biochem.ucl.ac.uk/bsm/',
184 'clustal' =>'http://www.csc.fi/molbio/progs/clustalw/clustalw.html',
185 'ebi' =>'http://www.ebi.ac.uk/',
186 'emotif' =>'http://motif.Stanford.EDU/emotif',
187 'entrez' =>'http://www3.ncbi.nlm.nih.gov/Entrez/',
188 'expasy' =>'http://www.expasy.ch/',
189 'gdb' =>'http://www.gdb.org/', # R.I.P. (Jan 1998); site still functional
190 'mips' =>'http://speedy.mips.biochem.mpg.de/',
191 'mmdb' =>'http://www.ncbi.nlm.nih.gov/Structure/',
192 'modbase' =>'http://guitar.rockefeller.edu/',
193 'ncbi' =>'http://www.ncbi.nlm.nih.gov/',
194 'pedant' =>'http://pedant.mips.biochem.mpg.de',
195 'phylip' =>'http://evolution.genetics.washington.edu/phylip.html',
196 'pir' =>'http://www-nbrf.georgetown.edu/pir/',
197 'pfam' =>'http://pfam.wustl.edu/',
198 'pfam_uk' =>'http://www.sanger.ac.uk/Software/Pfam/',
199 'pfam_us' =>'http://pfam.wustl.edu/',
200 'pdb' =>'http://www.pdb.bnl.gov/',
201 'presage' =>'http://presage.stanford.edu/',
202 'geneQuiz' =>'http://www.sander.ebi.ac.uk/genequiz/genomes/sc/',
203 'molMov' =>'http://bioinfo.mbb.yale.edu/MolMovDB/',
204 # 'protMot' =>'http://bioinfo.mbb.yale.edu/ProtMotDB/', # old, use molMov instead
205 'pubmed' =>'http://www.ncbi.nlm.nih.gov/PubMed/',
206 'sacch3d' =>'http://genome-www.stanford.edu/Sacch3D/',
207 'sgd' =>'http://genome-www.stanford.edu/Saccharomyces/',
208 # 'scop' =>'http://www.pdb.bnl.gov/scop/',
209 'scop' =>'http://scop.stanford.edu/scop/',
210 'swissProt' =>'http://www.expasy.ch/sprot/sprot-top.html',
211 'webmol' =>'http://genome-www.stanford.edu/structure/webmol/',
212 'ypd' =>'http://quest7.proteome.com/YPDhome.html',
213 );
214
215 ### Database access CGI stems. (For some DBs the home URL can be used as the CGI stem)
216 my %Stem_url =
217 (
218 'emotif' =>'http://dna.Stanford.EDU/cgi-bin/emotif/',
219 'entrez' =>'http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?',
220 'pdb' =>'http://www.pdb.bnl.gov/pdb-bin/',
221 'pfam_uk' =>'http://www.sanger.ac.uk/cgi-bin/Pfam/',
222 'pfam_us' =>'http://pfam.wustl.edu/cgi-bin/',
223 'pir' =>'http://www-nbrf.georgetown.edu/cgi-bin/nbrfget?',
224 );
225
226
227 ### Database access stems/links.
228 my %Search_url =
229 ( #'3db' =>'http://pdb.pdb.bnl.gov/cgi-bin/pdbids?3DB_ID=', # Former stem
230 '3db' =>$Stem_url{'pdb'}.'opdbshort?oPDBid=', # New stem (aug 1997)
231 'embl' =>$Home_url{'ebi'}.'htbin/emblfetch?',
232 'expasy' =>$Home_url{'expasy'}.'cgi-bin/', # program name and query string must be supplied.
233 'cath' =>$Home_url{'bsm'}.'cath/CATHSrch.pl?type=PDB&query=',
234 'cog_seq' =>$Home_url{'ncbi'}.'cgi-bin/COG/nph-cognitor?seq=', # add sequence
235 # To cog_orf, append ORF name ('YAL005c'). Case-sensitive! YAL005C won't work!
236 'cog_orf' =>$Home_url{'ncbi'}.'cgi-bin/COG/cogeseq?',
237 'ec1' =>$Home_url{'gdb'}.'bin/bio/wais_q-bio?object_class_key=30&jhu_id=',
238 'ec2' =>$Home_url{'bsm'}.'enzymes/',
239 'ec3' =>$Home_url{'expasy'}.'cgi-bin/get-enzyme-entry?',
240 'emotif_id' =>$Stem_url{'emotif'}.'nph-identify?sequence=',
241 'entrez' =>$Stem_url{'entrez'}."db=p_r?db=1&choseninfo=ORF_NAME%20[Gene%20Name]\@1\@1&form=4&field=Gene%20Name&mode=0&retrievestring=ORF_NAME%20[Gene%20Name]",
242 'gb_n' =>$Stem_url{'entrez'}."db=n&form=6&dopt=g&uid=",
243 'gb_p' =>$Stem_url{'entrez'}."db=p&form=6&dopt=g&uid=",
244 'gb_struct' =>$Stem_url{'entrez'}."db=t&form=6&dopt=s&uid=",
245 'pdb' =>$Stem_url{'pdb'}.'send-text?filename=',
246 'medline' =>$Stem_url{'entrez'}.'form=6&db=m&Dopt=r&uid=',
247 'mmdb' =>$Stem_url{'entrez'}.'db=t&form=6&Dopt=s&uid=',
248 'modbase_orf' =>$Home_url{'modbase'}.'gm-cgi-bin/orf_page.cgi?pg1=0.5&pg2=1.0&orf=',
249 # To the modbase_model, append yeast ORF name &pdb=<4-LETTER_CODE>&chain=<UPCASE LETTER, IF ANY>
250 'modbase_model' =>$Home_url{'modbase'}.'gm-cgi-bin/model_page.cgi?pg1=0.5&pg2=1.0&orf=',
251 'molMov' =>$Home_url{'molMov'}.'search.cgi?pdb=',
252 'pdb' =>$Stem_url{'pdb'}.'opdbshort?oPDBid=', # same as 3db
253 'pdb_coord' =>$Stem_url{'pdb'}.'send-pdb?filename=', # retrieves full coordinate file
254 'pfam' =>$Home_url{'pfam'}.'cgi-bin/nph-hmm_search?evalue=1.0&protseq=', # default: seq search, US
255 'pfam_sp_uk' =>$Stem_url{'pfam_uk'}.'swisspfamget.pl?name=',
256 'pfam_seq_uk' =>$Stem_url{'pfam_uk'}.'nph-search.cgi?evalue=1.0&type=normal&protseq=',
257 'pfam_sp_us' =>$Stem_url{'pfam_us'}.'getswisspfam?key=',
258 'pfam_seq_us' =>$Stem_url{'pfam_us'}.'nph-hmm_search?evalue=1.0&protseq=',
259 'pfam_form' =>$Home_url{'pfam'}.'cgi-bin/hmm_page.cgi', # interactive search form
260 'pir_id' =>$Stem_url{'pir'}.'fmt=c&xref=0&id=',
261 'pir_acc' =>$Stem_url{'pir'}.'fmt=c&xref=1&id=',
262 'pir_uid' =>$Stem_url{'pir'}.'uid=',
263 'pdbSum' =>$Home_url{'bsm'}.'cath/GetPDBSUMCODE.pl?code=',
264 # 'protMot' =>$Home_url{'protMot'}.'search.cgi?pdb=', # old, use molMov instead
265 'presage_sp' =>$Home_url{'presage'}.'search.cgi?spac=',
266 'swpr' =>$Home_url{'expasy'}.'cgi-bin/get-sprot-entry?',
267 'swModel' =>$Home_url{'expasy'}.'cgi-bin/sprot-swmodel-sub?',
268 'swprSearch' =>$Home_url{'expasy'}.'cgi-bin/sprot-search-ful?',
269
270 ### SCOP tlev options can be appended to the stem after adding a PDB ID.
271 ### tlev options are: 'dm'(domain), 'sf'(superfamily), 'fa'(family), 'cf'(common fold), 'cl'(class)
272 ### E.g., search.cgi?pdb=1ARD;tlev=dm
273
274 'scop' =>$Home_url{'scop'}.'search.cgi?pdb=', ### better to use scop_pdb.
275 'scop_pdb' =>$Home_url{'scop'}.'search.cgi?pdb=',
276 'scop_data' =>$Home_url{'scop'}.'data/scop.', ### Deprecated: frequent changes.
277
278 ## Search URLs for SGD/Sacch3D are contained %SGD_url and %S3d_url (below).
279
280 # For wormpep, the query string MUST end with "&keyword=" (after appending a sequence ID)
281 'wormpep' =>'http://www.sanger.ac.uk/cgi-bin/wormpep_fetch.pl?entry=',
282 'wormace' =>'http://webace.sanger.ac.uk/cgi-bin/webace?db=wormace&class=Sequence&text=yes&object=',
283
284 ### YPD: You must use a valid gene name or ORF name (IFF there is no gene name).
285 ### For this reason it is most convenient to use SGD's Protein_Info link
286 ### which can accept either and will provide a proper link to YPD.
287 'ypd' =>'http://quest7.proteome.com/YPD/',
288 );
289
290
291
292 ### CGI stems for SGD and Sacch3D.
293 my %SGD_stem_url =
294 ('stanford' =>'http://genome-www.stanford.edu/',
295 'sgd' =>'http://genome-www.stanford.edu/cgi-bin/SGD/',
296 'sgd2' =>'http://genome-www2.stanford.edu/cgi-bin/SGD/',
297 's3d' =>'http://genome-www.stanford.edu/cgi-bin/SGD/Sacch3D/',
298 's3d2' =>'http://genome-www2.stanford.edu/cgi-bin/SGD/Sacch3D/',
299 's3d3' =>'http://genome-www3.stanford.edu/cgi-bin/SGD/Sacch3D/',
300 'sacchdb' =>'http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?',
301 );
302
303 ### SGD stems and links.
304 my %SGD_url =
305 ('home' =>$Home_url{'sgd'},
306 'help' =>$Home_url{'sgd'}.'help/',
307 'mammal' =>$Home_url{'sgd'}.'mammal/',
308 'worm' =>$Home_url{'sgd'}.'worm/',
309 'gene' =>$SGD_stem_url{'sacchdb'}.'find+Locus+',
310 'locus' =>$SGD_stem_url{'sacchdb'}.'find+Locus+',
311 'orf' =>$SGD_stem_url{'sacchdb'}.'find+Locus+',
312 'mipsorf' =>$SGD_stem_url{'sgd'}."mips-orfs?",
313 'gene_info' =>$SGD_stem_url{'sacchdb'}.'find+Gene_Info+',
314 'prot_info' =>$SGD_stem_url{'sacchdb'}.'find+Protein_Info+',
315 'seq' =>$SGD_stem_url{'sgd'}.'seqDisplay?seq=',
316 'gi' =>$SGD_stem_url{'sacchdb'}.'find+Sequence+Database+=+GenPept+AND+NEXT+=+',
317 'chr' =>$SGD_stem_url{'sgd2'}.'seqTools?chr=',
318 'chr_old' =>$SGD_stem_url{'sgd'}.'dnaredir?chr=',
319 'seq_an' =>$SGD_stem_url{'sgd2'}.'seqTools?seqname=',
320 'seq_an_old' =>$SGD_stem_url{'sgd'}.'dnaredir?seqname=',
321 'map_chr' =>$SGD_stem_url{'sgd'}.'ORFMAP/ORFmap?chr=',
322 'map_orf' =>$SGD_stem_url{'sgd'}.'ORFMAP/ORFmap?seq=',
323 # 'chr' =>$SGD_stem_url{'sgd2'}.'seqform?chr=',
324 # 'seg' =>$SGD_stem_url{'sgd2'}.'seqform?seg=',
325 # 'fea' =>$SGD_stem_url{'sgd2'}.'featureform?seg=',
326 'feature' =>$SGD_stem_url{'sgd2'}.'featureform?chr=', # complete with "5&beg=100&end=400"
327 'search' =>$SGD_stem_url{'sgd'}.'search?',
328 'images' =>$SGD_stem_url{'stanford'}.'images/',
329 'suggest' =>$SGD_stem_url{'stanford'}.'forms/sgd-suggestion.html',
330 'tmp' =>$SGD_stem_url{'stanford'}.'tmp/',
331 );
332
333
334 ### Sacch3D stems and links.
335 my %S3d_url =
336 ('home' =>$Home_url{'sacch3d'},
337 'search' =>$Home_url{'sacch3d'}.'search.html',
338 'help' =>$Home_url{'sacch3d'}.'help/',
339 'new' =>$Home_url{'sacch3d'}.'new/',
340 'chrm' =>$Home_url{'sacch3d'}.'data/chr',
341 'domains' =>$Home_url{'sacch3d'}.'domains/',
342 'genequiz' =>$Home_url{'sacch3d'}.'genequiz/',
343 'analysis' =>$Home_url{'sacch3d'}.'analysis/',
344 'scop' =>$SGD_stem_url{'s3d3'}.'getscop?data=',
345 'scop_fold' =>$SGD_stem_url{'s3d3'}.'getscop?type=fold&data=',
346 'scop_class' =>$SGD_stem_url{'s3d3'}.'getscop?type=class&data=',
347 'scop_gene' =>$SGD_stem_url{'s3d3'}.'getscop?type=gene&data=',
348 'gene' =>$SGD_stem_url{'s3d'}.'get?class=gene&item=',
349 'orf' =>$SGD_stem_url{'s3d'}.'get?class=orf&item=',
350 'text' =>$SGD_stem_url{'s3d'}.'get?class=text&item=',
351 'pdb' =>$SGD_stem_url{'s3d'}.'get?class=pdb&item=',
352 'pdb_coord' =>$SGD_stem_url{'s3d'}.'pdbcoord.pl?id=',
353 'dsc' =>$SGD_stem_url{'s3d'}.'dsc.pl?gene=',
354 'emotif' =>$SGD_stem_url{'s3d'}.'seq_search.pl?db=emotif&gene=',
355 'pfam' =>$SGD_stem_url{'s3d'}.'seq_search.pl?db=pfam&gene=',
356 'pfam_uk' =>$SGD_stem_url{'s3d'}.'seq_search.pl?db=pfam&loc=uk&gene=',
357 'pfam_us' =>$SGD_stem_url{'s3d'}.'seq_search.pl?db=pfam&loc=us&gene=',
358 'blast_pdb' =>$SGD_stem_url{'s3d'}.'getblast?db=pdb&name=',
359 'blast_nr' =>$SGD_stem_url{'s3d'}.'getblast?db=nr&name=',
360 'blast_est' =>$SGD_stem_url{'s3d'}.'getblast?db=est&name=',
361 'blast_mammal' =>$SGD_stem_url{'s3d'}.'getblast?db=mammal&name=',
362 'blast_human' =>$SGD_stem_url{'s3d'}.'getblast?db=human&name=',
363 'blast_worm' =>$SGD_stem_url{'s3d'}.'getblast?db=worm&name=',
364 'blast_yeast' =>$SGD_stem_url{'s3d'}.'getblast?db=yeast&name=',
365 'blast_worm_yeast'=>$SGD_stem_url{'s3d'}.'getblast?db=worm&query=worm&name=',
366 'patmatch' =>$SGD_stem_url{'s3d2'}.'grepmatch?', ## deprecated
367 'grepmatch' =>$SGD_stem_url{'s3d2'}.'grepmatch?',
368 'pdb_neighbors' =>$SGD_stem_url{'s3d'}.'pdb_neighbors?id=CHAIN&gene=ORF_NAME',
369 );
370
371
372 ### 3D viewer stems.
373 my %Viewer_url =
374 # ('java' =>$SGD_stem_url{'sgd'}.'Sacch3D/pdbViewer.pl?pdbCode=PDB&orf=',
375 (
376 'java' =>$SGD_stem_url{'sgd'}.'Sacch3D/pdbViewer.pl?pdbCode=', # Default java viewer
377 'webmol' =>$SGD_stem_url{'sgd'}.'Sacch3D/pdbViewer.pl?pdbCode=',
378 'codebase' =>$SGD_stem_url{'stanford'}.'structure/webmol/lib',
379 'rasmol' =>$Stem_url{'pdb'}.'send-ras?filename=',
380 'chime' =>$Stem_url{'pdb'}.'ccpeek?id=',
381 'cn3d' =>$Stem_url{'entrez'}.'db=t&form=6&Dopt=i&Complexity=Cn3D+Subset&uid=',
382 'kinemage' =>'http://prosci.org/Kinemage',
383 );
384
385
386 ### Stock HTML
387 # The error reporting HTML strings represent some experiments in human psychology:
388 # how do you induce users to report errors that you should know about yet not
389 # get flooded with trivial problems caused by novices?
390 my %Html =
391 ('authority' =>qq|<A HREF="mailto:$AUTHORITY"><b>$AUTHORITY</b></A>|,
392 'trouble' => <<"QQ_TROUBLE_QQ",
393 <p>If this problem persists, <A HREF="mailto:$AUTHORITY"><b>please notify us.</b></A>
394 Include a copy of this error page with your message. Thanks.<p>
395 QQ_TROUBLE_QQ
396 'notify' => <<"QQ_NOTIFY_QQ",
397 <A HREF="mailto:$AUTHORITY"><b>Please notify us.</b></A>
398 Include a copy of this error page with your message. Thanks.<p>
399 QQ_NOTIFY_QQ
400 'ourFault' => <<"QQ_FAULT_QQ",
401 <p><b>This is our fault!</b> There is apparently a problem with our software
402 that we may not know about. <A HREF="mailto:$AUTHORITY"><b>Please notify us!</b></A>
403 Include a copy of this error page with your message. Thanks.<p>
404 QQ_FAULT_QQ
405 'techDiff' => <<"QQ_TECH_QQ",
406 <p><big>We are experiencing technical difficulties now.<br>
407 We will have the problem fixed soon. Sorry for any inconvenience.</big><p>
408 QQ_TECH_QQ
409
410 );
411
412
413 ### Miscellaneous URLs. Configure as desired for your site.
414 my $Not_found_url = 'http://genome-www.stanford.edu/Sacch3D/notfound.html';
415 my $Tmp_url = 'http://genome-www.stanford.edu/tmp/';
416
417
418
419 =head1 APPENDIX
420
421 Methods beginning with a leading underscore are considered private
422 and are intended for internal use by this module. They are
423 B<not> considered part of the public interface and are described here
424 for documentation purposes only.
425
426 =cut
427
428 #########################################################################
429 ## ACCESSOR METHODS
430 #########################################################################
431
432
433 =head2 home_url
434
435 Usage : $BioWWW->home_url(<string>)
436 Purpose : To obtain the homepage URL for a biological database or resource.
437 Returns : String containing the URL (including "http://")
438 Argument : String
439 : Currently acceptable arguments are:
440 : bioperl bioperl-schema biomoo bsm ebi emotif entrez
441 : expasy mips mmdb ncbi pir pfam pdb geneQuiz
442 : molMov pubmed sacch3d sgd scop swissProt webmol ypd
443 Throws : Warns if argument cannot be resolved to a URL.
444 Comments : The URLs listed here do not represent a complete list.
445 : Expect this to evolve and grow with time.
446
447 See Also : L<search_url>()
448
449 =cut
450
451 #-------------
452 sub home_url {
453 #-------------
454 my($self,$arg) = @_;
455 $arg eq 'all' and return %Home_url;
456 (exists $Home_url{$arg}) ? $Home_url{$arg}
457 : ($self->warn("Can't resolve argument to URL: $arg"),
458 $Not_found_url);
459 }
460
461
462
463 =head2 search_url
464
465 Usage : $BioWWW->search_url(<string>)
466 Purpose : To provide a URL stem for a search engine at a biological database
467 : or resource.
468 Returns : String containing the URL (including "http://")
469 Argument : String
470 : Currently acceptable arguments are:
471 : 3db embl cath ec1 ec2 ec3 emotif_id entrez gb1 gb2
472 : gb3 gb4 gb5 pdb medline mmdb pdb pdb_coord pfam pir_acc
473 : pdbSum molMov swpr swModel swprSearch scop scop_pdb scop_data
474 : ypd
475 Throws : Warns if argument cannot be resolved to a URL.
476 Comments : Unlike the homepage URLs, this method does not return a complete
477 : URL but a stem which must be further modified, typically by
478 : appending data to it, before it can be used. The data appended
479 : depends on the specific URL; typically, it is a database ID or
480 : other unique identifier.
481 : The requirements for each URL will be described here eventually.
482 :
483 : The URLs listed here do not represent a complete list.
484 : Expect this to evolve and grow with time.
485 :
486 : Given this complexity, it may be useful to provide special methods
487 : for these different URLs. This would however result in an
488 : explosion of methods that might make this module less
489 : maintainable and harder to use.
490
491 See Also : L<home_url>()
492
493 =cut
494
495 #--------------
496 sub search_url {
497 #--------------
498 my($self,$arg) = @_;
499 $arg eq 'all' and return %Search_url;
500 (exists $Search_url{$arg}) ? $Search_url{$arg}
501 : ($self->warn("Can't resolve argument to URL: $arg"),
502 $Not_found_url);
503 }
504
505
506
507 =head2 stem_url
508
509 Usage : $BioWWW->stem_url(<string>)
510 Purpose : To obtain the minimal stem URL for searching a biological database or resource.
511 Returns : String containing the URL (including "http://")
512 Argument : String
513 : Currently acceptable arguments are:
514 : emotif entrez pdb
515 Throws : Warns if argument cannot be resolved to a URL.
516 Comments : The URLs stems returned by this method are much more minimal than
517 : this provided by search_url(). Use of these stems requires knowledge
518 : of the CGI scripts which they invoke.
519
520 See Also : L<search_url>()
521
522 =cut
523
524 #--------------
525 sub stem_url {
526 #--------------
527 my($self,$arg) = @_;
528 $arg eq 'all' and return %Stem_url;
529 (exists $Stem_url{$arg}) ? $Stem_url{$arg}
530 : ($self->warn("Can't resolve argument to URL: $arg"),
531 $Not_found_url);
532 }
533
534
535
536 =head2 viewer_url
537
538 Usage : $BioWWW->viewer_url(<string>)
539 Purpose : To obtain the stem URL for a 3D viewer (RasMol, WebMol, Cn3D)
540 Returns : String containing the URL (including "http://")
541 Argument : String
542 : Currently acceptable arguments are:
543 : rasmol webmol cn3d java (java is an alias for webmol)
544 Throws : Warns if argument cannot be resolved to a URL.
545 Comments : The 4-letter Brookhaven PDB identifier must be appended to the
546 : URL provided by this method.
547 : The URLs listed here do not represent a complete list.
548 : Expect this to evolve and grow with time.
549
550 =cut
551
552 #---------------
553 sub viewer_url {
554 #---------------
555 my($self,$arg) = @_;
556 $arg eq 'all' and return %Viewer_url;
557 (exists $Viewer_url{$arg}) ? $Viewer_url{$arg}
558 : ($self->warn("Can't resolve argument to URL: $arg"),
559 $Not_found_url);
560 }
561
562
563
564 =head2 not_found_url
565
566 Usage : $BioWWW->not_found_url()
567 Purpose : To obtain the URL for a web page to be shown in place of a 404 error.
568 Returns : String containing the URL (including "http://")
569 Argument : n/a
570 Throws : n/a
571 Comments : This URL should be customized as desired.
572
573 =cut
574
575 #-----------------
576 sub not_found_url { my $self = shift; $Not_found_url; }
577 #-----------------
578
579
580 =head2 tmp_url
581
582 Usage : $BioWWW->tmp_url()
583 Purpose : To obtain the URL for a temporary, web-accessible directory.
584 Returns : String containing the URL (including "http://")
585 Argument : n/a
586 Throws : n/a
587 Comments : This URL should be customized as desired.
588
589 =cut
590
591 #-----------
592 sub tmp_url { my $self = shift; $Tmp_url; }
593 #-----------
594
595
596
597 =head2 search_link
598
599 Usage : $BioWWW->search_link(<site>, <value>, <text>)
600 Purpose : Wrapper for search_url() that returns the URL within an HTML anchor.
601 Returns : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
602 Argument : <site> = string to be used as argument for search_url()
603 : <value> = string to be appended to the search URL stem.
604 : <text> = string to be shown as the link text (default = <value>).
605 Throws : n/a
606 Status : Experimental
607
608 See Also : L<search_url>()
609
610 =cut
611
612 #---------------
613 sub search_link {
614 #---------------
615 my($self,$arg,$value,$text) = @_;
616 my $url = $self->search_url($arg);
617 $text ||= $value;
618 qq|<A HREF="$url$value">$text</A>|;
619 }
620
621
622
623 =head2 viewer_link
624
625 Usage : $BioWWW->viewer_link(<site>, <value>, <text>)
626 Purpose : Wrapper for viewer_url() that returns the complete URL within an HTML anchor.
627 Returns : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
628 Argument : <site> = string to be used as argument for viewer_url()
629 : <value> = string to be appended to the viewer URL stem.
630 : <text> = string to be shown as the link text (default = <value>).
631 Throws : n/a
632 Status : Experimental
633
634 See Also : L<viewer_url>()
635
636 =cut
637
638 #----------------
639 sub viewer_link {
640 #----------------
641 my($self,$arg,$value,$text) = @_;
642 my $url = $self->viewer_url($arg);
643 $text ||= $value;
644 qq|<A HREF="$url$value">$text</A>|;
645 }
646
647
648
649 =head2 html
650
651 Usage : $BioWWW->html(<string>)
652 Purpose : To obtain HTML-formatted text for frequently needed web-page messages.
653 Returns : String containing the HTML anchor ( qq|<A HREF="http://..."</A>|)
654 Argument : String.
655 : Currently acceptable arguments are:
656 : authority (mailto: link for webmaster; shows e-mail address as link)
657 : notify (wraps mailto:authority link with text for link "please notify us")
658 : ourFault ("this problem is our fault. If it persists <notify-link>")
659 : trouble (same as ourFault but doesn't blame us for the problem)
660 : techDiff ("we are experiencing technical difficulties. Please stand by.")
661 Throws : n/a
662 Comments : The authority (webmaster) is imported from the Bio::Root::Global.pm
663 : module. The value for $AUTHORITY should be set there, or
664 : customize this module so that it doesn't use Bio::Root::Global.pm.
665
666 =cut
667
668 #----------
669 sub html {
670 #----------
671 my($self,$arg) = @_;
672 $arg eq 'all' and return %Html;
673 (exists $Html{$arg}) ? $Html{$arg} : "<pre>(missing HTML for \"$arg\")</pre>";
674 }
675
676
677 ###
678 ### Below are accessors specialized for the Saccharomyces Genome Database
679 ### It is possible that they will be moved to Bio::SGD::WWW.pm in the future.
680 ###
681
682
683 =head2 sgd_url
684
685 Usage : $BioWWW->sgd_url(<string>)
686 Purpose : To obtain the webpage URL or search stem for SGD.
687 Returns : String containing the URL (including "http://")
688 Argument : String
689 : Currently acceptable arguments (TODO).
690 Throws : Warns if argument cannot be resolved to a URL.
691 Comments : This accessor is specialized for the Saccharomyces Genome Database.
692 : It is possible that it will be moved to SGD::WWW.pm in the future.
693
694 See Also : L<search_url>()
695
696 =cut
697
698 #------------
699 sub sgd_url {
700 #------------
701 my($self,$arg) = @_;
702 $arg eq 'all' and return %SGD_url;
703 (exists $SGD_url{$arg}) ? $SGD_url{$arg}
704 : ($self->warn("Can't resolve argument to URL: $arg"),
705 $Not_found_url);
706 }
707
708
709
710 =head2 s3d_url
711
712 Usage : $BioWWW->s3d_url(<string>)
713 Purpose : To obtain the webpage URL or search stem for Sacch3D.
714 Returns : String containing the URL (including "http://")
715 Argument : String
716 : Currently acceptable arguments (TODO).
717 Throws : Warns if argument cannot be resolved to a URL.
718 Comments : This accessor is specialized for the Saccharomyces Genome Database.
719 : It is possible that it will be moved to SGD::WWW.pm in the future.
720
721 See Also : L<search_url>()
722
723 =cut
724
725 #-----------
726 sub s3d_url {
727 #-----------
728 my($self,$arg) = @_;
729 $arg eq 'all' and return %S3d_url;
730 (exists $S3d_url{$arg}) ? $S3d_url{$arg}
731 : ($self->warn("Can't resolve argument to URL: $arg"),
732 $Not_found_url);
733 }
734
735
736
737 =head2 sgd_stem_url
738
739 Usage : $BioWWW->sgd_stem_url(<string>)
740 Purpose : To obtain the minimal stem URL for a SGD/Sacch3D CGI script.
741 Returns : String containing the URL (including "http://")
742 Argument : String
743 : Currently acceptable arguments (TODO).
744 Throws : Warns if argument cannot be resolved to a URL.
745 Comments : This accessor is specialized for the Saccharomyces Genome Database.
746 : It is possible that it will be moved to SGD::WWW.pm in the future.
747
748 See Also : L<search_url>()
749
750 =cut
751
752 #-----------------
753 sub sgd_stem_url {
754 #-----------------
755 my($self,$arg) = @_;
756 $arg eq 'all' and return %SGD_stem_url;
757 (exists $SGD_stem_url{$arg}) ? $SGD_stem_url{$arg}
758 : ($self->warn("Can't resolve argument to URL: $arg"),
759 $Not_found_url);
760 }
761
762
763
764 =head2 s3d_link
765
766 Usage : $BioWWW->s3d_link(<site>, <value>, <text>)
767 Purpose : Wrapper for s3d_url() that returns the complete URL within an HTML anchor.
768 Returns : String containing the URL (including "http://")
769 Argument : <site> = string to be used as argument for s3d_url()
770 : <value> = string to be appended to the s3d URL stem.
771 : <text> = string to be shown as the link text (default = <value>).
772 Throws : n/a
773 Status : Experimental
774 Comments : This accessor is specialized for the Saccharomyces Genome Database.
775 : It is possible that it will be moved to SGD::WWW.pm in the future.
776
777 See Also : L<s3d_url>(), L<sgd_link>()
778
779 =cut
780
781 #--------------
782 sub s3d_link {
783 #--------------
784 my($self,$arg,$value,$text) = @_;
785 my $url = $self->s3d_url($arg);
786 $text ||= $value;
787 qq|<A HREF="$url$value">$text</A>|;
788 }
789
790
791
792 =head2 sgd_link
793
794 Usage : $BioWWW->sgd_link(<site>, <value>, <text>)
795 Purpose : Wrapper for sgd_url() that returns the complete URL within an HTML anchor.
796 Returns : String containing the URL (including "http://")
797 Argument : <site> = string to be used as argument for sgd_url()
798 : <value> = string to be appended to the sgd URL stem.
799 : <text> = string to be shown as the link text (default = <value>).
800 Throws : n/a
801 Status : Experimental
802 Comments : This accessor is specialized for the Saccharomyces Genome Database.
803 : It is possible that it will be moved to SGD::WWW.pm in the future.
804
805 See Also : L<sgd_url>(), L<s3d_link>()
806
807 =cut
808
809 #--------------
810 sub sgd_link {
811 #--------------
812 my($self,$arg,$value,$text) = @_;
813 my $url = $self->sgd_url($arg);
814 $text ||= $value;
815 qq|<A HREF="$url$value">$text</A>|;
816 }
817
818
819 #########################################################################
820 ## INSTANCE METHODS
821 #########################################################################
822
823 ## Note that similar functions to those presented below are also availble
824 ## via L. Stein's CGI.pm. These are more experimental versions.
825
826 =head2 start_html
827
828 Usage : $BioWWW->start_html()
829 Purpose : Prints the "Content-type: text/html\n\n<HTML>\n" header.
830 Returns : n/a; This method prints the Content-type string shown above.
831 Argument : n/a
832 Throws : n/a
833 Status : Experimental
834 Comments : This method prevents redundant invocations thus avoiding th
835 : accidental printing of the "content-type..." on the page.
836 : If using L. Stein's CGI.pm, this is similar to $query->header()
837 : (Does CGI.pm prevent redundant invocation?)
838
839 =cut
840
841 #---------------'
842 sub start_html {
843 #---------------
844 my $self=shift;
845 if(!$self->{'_started_html'}) {
846 print "Content-type: text/html\n\n<HTML>\n";
847 $self->{'_started_html'} = 1;
848 }
849 }
850
851
852 =head2 redirect
853
854 Usage : $BioWWW->redirect(<string>)
855 Purpose : Prints the header needed to redirect a web browser to a supplied URL.
856 Returns : n/a; Prints the redirection header.
857 Argument : String containing the URL to be redirected to.
858 Throws : n/a
859 Status : Experimental
860
861 =cut
862
863 #-------------
864 sub redirect {
865 #-------------
866 my($self,$url) = @_;
867
868 print "Location: $url\n";
869 print "Content-type: text/html\n\n";
870 }
871
872
873
874 =head2 pre
875
876 Usage : $BioWWW->pre("text to be pre-formatted");
877 Purpose : To produce HTML for text that is not to be formated by the brower.
878 Returns : String containing the "<pre>" formatted html.
879 Argument : n/a
880 Throws : n/a
881 Status : Experimental
882
883 =cut
884
885 #--------
886 sub pre {
887 #--------
888 my $self = shift;
889 "<PRE>\n".shift()."\n</PRE>";
890 }
891
892
893 #----------------
894 sub html_footer {
895 #----------------
896 my( $self, @param ) = @_;
897
898 my( $linkTo, $linkText, $modified, $mail, $mailText, $top) =
899 $self->_rearrange([qw(LINKTO LINKTEXT MODIFIED MAIL MAILTEXT TOP)], @param);
900
901 $modified = (scalar $modified)
902 ? qq|<center><small><b>Last modified: $modified </b></small></center>|
903 : '';
904
905 $linkTo ||= '';
906
907 # $top = (defined $top) ? qq|<a href="top">Top</a><br>| : '';
908 $top = qq|<a href="#top">Top</a>|; ## Utilizing the HTML bug/feature wherein
909 ## a bogus name anchor defaults to the
910 ## top of the page.
911
912 return <<"HTML";
913 <p>
914 <hr size=3 noshade width=95%>
915 $top | <a href="$linkTo"> $linkText</a><br>
916 $modified
917 <small><i><a href="mailto:$mail">$mailText</a></i></small>
918 </body></html>
919
920 HTML
921 }
922
923
924 =head2 strip_html
925
926 Usage : $boolean = &strip_html( string_ref, [fast] );
927 Purpose : Removes HTML formatting from a supplied string.
928 Returns : Boolean: true if string was stripped, false if not.
929 Argument : string_ref = reference to a string containing the whole
930 : web page to be stripped.
931 : fast = a non-zero value. Optional. If set, a faster
932 : but perhaps less thorough procedure is used for
933 : stripping. Default = not fast.
934 Throws : Exception if the argument is not a scalar reference.
935 Comments : Based on code originally written by Alex Dong Li
936 : (ali@genet.sickkids.on.ca).
937 : This is a more generic version of the function that appears
938 : in Bio::Tools::Blast::HTML.pm
939 : This version does not perform any Blast-specific stripping.
940 :
941 : This employs a simple method for removing tags that
942 : will fail under following conditions:
943 : 1) if quoted > appears in a tag (does this ever happen?)
944 : 2) if a tag is split over multiple lines and this method is
945 : used to process one line at a time.
946 :
947 : Without fast mode, large HTML files can take exceedingly long times to
948 : strip (e.g., 1Meg file with many tags can take 10 minutes versus 5 seconds
949 : in fast mode. Try the swissprot yeast table). If you know the HTML to be
950 : well-behaved (i.e., tags are not split across mutiple lines), use fast
951 : mode for large, dense files.
952
953 =cut
954
955 #---------------
956 sub strip_html {
957 #---------------
958 my ($self, $string_ref, $fast) = @_;
959
960 ref $string_ref eq 'SCALAR' or
961 $self->throw("Can't strip HTML: ".
962 "Argument is should be a SCALAR reference not a ${\ref $string_ref}");
963
964 my $str = $$string_ref;
965 my $stripped = 0;
966
967 if($fast) {
968 # MULTI-STRING-MODE: Much faster than single-string mode
969 # but will miss tags that span multiple lines.
970 # This is fine if you know the HTML to be "well-behaved".
971
972 my @lines = split("\n", $str);
973 foreach (@lines) {
974 s/<[^>]+>|&nbsp//gi and $stripped = 1;
975 }
976
977 # This regexp likely won't work properly in this mode.
978 foreach (@lines) {
979 s/(\A|\n)>\s+/\n\n>/gi and $stripped = 1;
980 }
981 $$string_ref = join ("\n", @lines);
982
983 } else {
984
985 # SINGLE-STRING-MODE: Can be very slow for long strings with many substitutions.
986
987 # Removing all "<>" tags.
988 $str =~ s/<[^>]+>|&nbsp//sgi and $stripped = 1;
989
990 # Re-uniting any lone '>' characters. Not really necessary for functional HTML
991 $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1;
992
993 $$string_ref = $str;
994 }
995 $stripped;
996 }
997
998
999 1;
1000 __END__
1001
1002 ########################################################################
1003 ## END OF CLASS
1004 ########################################################################
1005
1006 =head1 FOR DEVELOPERS ONLY
1007
1008 =head2 Data Members
1009
1010 An instance of Bio::Tools::WWW.pm is a blessed reference to a hash containing
1011 all or some of the following fields:
1012
1013 FIELD VALUE
1014 --------------------------------------------------------------
1015 _started_html Defined the on the initial invocation of start_html()
1016 to avoid duplicate printing out the "Content-type..." header.
1017
1018
1019 =cut
1020
1021 1;
1022
1023