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some pod cleaning

svn path=/bioperl-db/trunk/; revision=16205
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commit 26048f6138a8a9fa443248d597883a1f086b0157 1 parent c9d270e
authored September 29, 2009

Showing 64 changed files with 268 additions and 265 deletions. Show diff stats Hide diff stats

  1. 9  Build.PL
  2. 28  Changes
  3. 8  lib/Bio/BioEntry.pm
  4. 8  lib/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm
  5. 8  lib/Bio/DB/BioSQL/BaseDriver.pm
  6. 8  lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
  7. 8  lib/Bio/DB/BioSQL/BioNamespaceAdaptor.pm
  8. 8  lib/Bio/DB/BioSQL/BiosequenceAdaptor.pm
  9. 8  lib/Bio/DB/BioSQL/ClusterAdaptor.pm
  10. 8  lib/Bio/DB/BioSQL/CommentAdaptor.pm
  11. 8  lib/Bio/DB/BioSQL/DBLinkAdaptor.pm
  12. 8  lib/Bio/DB/BioSQL/LocationAdaptor.pm
  13. 8  lib/Bio/DB/BioSQL/OBDA.pm
  14. 8  lib/Bio/DB/BioSQL/OntologyAdaptor.pm
  15. 8  lib/Bio/DB/BioSQL/Oracle/AnnotationCollectionAdaptorDriver.pm
  16. 8  lib/Bio/DB/BioSQL/Oracle/BasePersistenceAdaptorDriver.pm
  17. 8  lib/Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm
  18. 8  lib/Bio/DB/BioSQL/Oracle/PathAdaptorDriver.pm
  19. 8  lib/Bio/DB/BioSQL/Oracle/SpeciesAdaptorDriver.pm
  20. 8  lib/Bio/DB/BioSQL/Oracle/TermAdaptorDriver.pm
  21. 8  lib/Bio/DB/BioSQL/PathAdaptor.pm
  22. 8  lib/Bio/DB/BioSQL/Pg/AnnotationCollectionAdaptorDriver.pm
  23. 8  lib/Bio/DB/BioSQL/Pg/BasePersistenceAdaptorDriver.pm
  24. 8  lib/Bio/DB/BioSQL/Pg/BiosequenceAdaptorDriver.pm
  25. 8  lib/Bio/DB/BioSQL/Pg/PathAdaptorDriver.pm
  26. 8  lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm
  27. 8  lib/Bio/DB/BioSQL/Pg/TermAdaptorDriver.pm
  28. 8  lib/Bio/DB/BioSQL/PrimarySeqAdaptor.pm
  29. 8  lib/Bio/DB/BioSQL/ReferenceAdaptor.pm
  30. 8  lib/Bio/DB/BioSQL/RelationshipAdaptor.pm
  31. 8  lib/Bio/DB/BioSQL/SeqAdaptor.pm
  32. 8  lib/Bio/DB/BioSQL/SeqFeatureAdaptor.pm
  33. 8  lib/Bio/DB/BioSQL/SimpleValueAdaptor.pm
  34. 8  lib/Bio/DB/BioSQL/SpeciesAdaptor.pm
  35. 8  lib/Bio/DB/BioSQL/TermAdaptor.pm
  36. 8  lib/Bio/DB/BioSQL/mysql/AnnotationCollectionAdaptorDriver.pm
  37. 8  lib/Bio/DB/BioSQL/mysql/BasePersistenceAdaptorDriver.pm
  38. 8  lib/Bio/DB/BioSQL/mysql/BiosequenceAdaptorDriver.pm
  39. 8  lib/Bio/DB/BioSQL/mysql/PathAdaptorDriver.pm
  40. 8  lib/Bio/DB/BioSQL/mysql/SpeciesAdaptorDriver.pm
  41. 8  lib/Bio/DB/BioSQL/mysql/TermAdaptorDriver.pm
  42. 8  lib/Bio/DB/CacheServer/SeqDB.pm
  43. 8  lib/Bio/DB/DBAdaptorI.pm
  44. 8  lib/Bio/DB/DBD.pm
  45. 8  lib/Bio/DB/DBI.pm
  46. 8  lib/Bio/DB/DBI/Oracle.pm
  47. 8  lib/Bio/DB/DBI/Pg.pm
  48. 8  lib/Bio/DB/DBI/Transaction.pm
  49. 8  lib/Bio/DB/DBI/TransactionListener.pm
  50. 8  lib/Bio/DB/DBI/base.pm
  51. 8  lib/Bio/DB/DBI/mysql.pm
  52. 8  lib/Bio/DB/PersistenceAdaptorI.pm
  53. 8  lib/Bio/DB/Persistent/BioNamespace.pm
  54. 8  lib/Bio/DB/Persistent/ObjectRelMapperI.pm
  55. 8  lib/Bio/DB/Persistent/PersistentObject.pm
  56. 8  lib/Bio/DB/Persistent/PersistentObjectFactory.pm
  57. 8  lib/Bio/DB/Persistent/PrimarySeq.pm
  58. 8  lib/Bio/DB/Persistent/Seq.pm
  59. 8  lib/Bio/DB/Persistent/SeqFeature.pm
  60. 8  lib/Bio/DB/PersistentObjectI.pm
  61. 8  lib/Bio/DB/Query/DBQueryResult.pm
  62. 8  lib/Bio/DB/Query/PrebuiltResult.pm
  63. 8  lib/Bio/DB/Query/QueryResultI.pm
  64. 8  lib/Bio/DB/SimpleDBContext.pm
9  Build.PL
@@ -18,12 +18,15 @@ my $build = Module::Build->new(
18 18
     license             => 'perl',
19 19
     requires            => {
20 20
                             'perl'               => '5.6.1',
21  
-                            'Bio::Root::Version' => '1.006009',
  21
+                            'Bio::Root::Version' => '1.006900',
22 22
                             'DBI'                => 0
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-                           },
  23
+        },
  24
+    recommends          => {
  25
+                            'Graph::Directed'   => 0
  26
+        },
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     get_options         => {
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                             accept  => { }
26  
-                           },
  29
+        },
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     dynamic_config      => 1,
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     create_makefile_pl  => 'passthrough'
29 32
 );
28  Changes
@@ -3,22 +3,22 @@ Revision history for bioperl-db.
3 3
 Full details of changes between all versions are available online at:
4 4
 http://www.bioperl.org/wiki/Change_log
5 5
 
  6
+1.6.x
  7
+------------------
  8
+* Convert back to simple Module::Build
  9
+* Now uses correct Bio::Species syntax [1.6.1]
  10
+
6 11
 1.5.2
7 12
 -----
8  
-Released with bioperl-1.5.2 developer branch release
9  
-
10  
-Introduced Build.PL as the recommended alternative to installation,
11  
-instead of Makefile.PL
12  
-
13  
-Compatability with bioperl-1.5.2 changes such as the new Bio::Species
  13
+* Released with bioperl-1.5.2 developer branch release
  14
+* Introduced Build.PL as the recommended alternative to installation, instead of
  15
+  Makefile.PL
  16
+* Compatability with bioperl-1.5.2 changes such as the new Bio::Species
14 17
 
15 18
 0.01
16 19
 ----
17  
-Ewan Birney's code committed to handle a simple relation schema
18  
-for roundtripping Genbank/EMBL (swissprot MOSTLY handled)
19  
-
20  
-Support built in for seqdb to serve as a BioCORBA seq caching server.
21  
-
22  
-Maps objects built on old schema - still in flux but included in release.
23  
-
24  
-Released with bioperl-0.7.2 stable branch release.
  20
+* Ewan Birney's code committed to handle a simple relation schema for
  21
+  roundtripping Genbank/EMBL (swissprot MOSTLY handled)
  22
+* Support built in for seqdb to serve as a BioCORBA seq caching server.
  23
+* Maps objects built on old schema - still in flux but included in release.
  24
+* Released with bioperl-0.7.2 stable branch release.
8  lib/Bio/BioEntry.pm
@@ -36,11 +36,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
36 36
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
37 37
 
38 38
 =head2 Support 
39  
- 
  39
+
40 40
 Please direct usage questions or support issues to the mailing list:
41  
-  
42  
-L<bioperl-l@bioperl.org>
43  
-  
  41
+
  42
+I<bioperl-l@bioperl.org>
  43
+
44 44
 rather than to the module maintainer directly. Many experienced and 
45 45
 reponsive experts will be able look at the problem and quickly 
46 46
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm
@@ -52,11 +52,11 @@ Your participation is much appreciated.
52 52
   bioperl-l@bio.perl.org
53 53
 
54 54
 =head2 Support 
55  
- 
  55
+
56 56
 Please direct usage questions or support issues to the mailing list:
57  
-  
58  
-L<bioperl-l@bioperl.org>
59  
-  
  57
+
  58
+I<bioperl-l@bioperl.org>
  59
+
60 60
 rather than to the module maintainer directly. Many experienced and 
61 61
 reponsive experts will be able look at the problem and quickly 
62 62
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/BaseDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/BioNamespaceAdaptor.pm
@@ -49,11 +49,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
49 49
   bioperl-l@bio.perl.org
50 50
 
51 51
 =head2 Support 
52  
- 
  52
+
53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
57 57
 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/BiosequenceAdaptor.pm
@@ -50,11 +50,11 @@ Your participation is much appreciated.
50 50
   bioperl-l@bio.perl.org
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/ClusterAdaptor.pm
@@ -48,11 +48,11 @@ Your participation is much appreciated.
48 48
   bioperl-l@bio.perl.org
49 49
 
50 50
 =head2 Support 
51  
- 
  51
+
52 52
 Please direct usage questions or support issues to the mailing list:
53  
-  
54  
-L<bioperl-l@bioperl.org>
55  
-  
  53
+
  54
+I<bioperl-l@bioperl.org>
  55
+
56 56
 rather than to the module maintainer directly. Many experienced and 
57 57
 reponsive experts will be able look at the problem and quickly 
58 58
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/CommentAdaptor.pm
@@ -51,11 +51,11 @@ Your participation is much appreciated.
51 51
   bioperl-l@bio.perl.org
52 52
 
53 53
 =head2 Support 
54  
- 
  54
+
55 55
 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
+
  57
+I<bioperl-l@bioperl.org>
  58
+
59 59
 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/DBLinkAdaptor.pm
@@ -51,11 +51,11 @@ Your participation is much appreciated.
51 51
   bioperl-l@bio.perl.org
52 52
 
53 53
 =head2 Support 
54  
- 
  54
+
55 55
 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
+
  57
+I<bioperl-l@bioperl.org>
  58
+
59 59
 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/LocationAdaptor.pm
@@ -53,11 +53,11 @@ Your participation is much appreciated.
53 53
   bioperl-l@bio.perl.org
54 54
 
55 55
 =head2 Support 
56  
- 
  56
+
57 57
 Please direct usage questions or support issues to the mailing list:
58  
-  
59  
-L<bioperl-l@bioperl.org>
60  
-  
  58
+
  59
+I<bioperl-l@bioperl.org>
  60
+
61 61
 rather than to the module maintainer directly. Many experienced and 
62 62
 reponsive experts will be able look at the problem and quickly 
63 63
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/OBDA.pm
@@ -44,11 +44,11 @@ Your participation is much appreciated.
44 44
   bioperl-l@bio.perl.org
45 45
 
46 46
 =head2 Support 
47  
- 
  47
+
48 48
 Please direct usage questions or support issues to the mailing list:
49  
-  
50  
-L<bioperl-l@bioperl.org>
51  
-  
  49
+
  50
+I<bioperl-l@bioperl.org>
  51
+
52 52
 rather than to the module maintainer directly. Many experienced and 
53 53
 reponsive experts will be able look at the problem and quickly 
54 54
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/OntologyAdaptor.pm
@@ -47,11 +47,11 @@ Your participation is much appreciated.
47 47
   bioperl-l@bio.perl.org
48 48
 
49 49
 =head2 Support 
50  
- 
  50
+
51 51
 Please direct usage questions or support issues to the mailing list:
52  
-  
53  
-L<bioperl-l@bioperl.org>
54  
-  
  52
+
  53
+I<bioperl-l@bioperl.org>
  54
+
55 55
 rather than to the module maintainer directly. Many experienced and 
56 56
 reponsive experts will be able look at the problem and quickly 
57 57
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/AnnotationCollectionAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/BasePersistenceAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/PathAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
+
53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
57 57
 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/SpeciesAdaptorDriver.pm
@@ -51,11 +51,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
51 51
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
52 52
 
53 53
 =head2 Support 
54  
- 
  54
+
55 55
 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
+
  57
+I<bioperl-l@bioperl.org>
  58
+
59 59
 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Oracle/TermAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
+
53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
57 57
 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/PathAdaptor.pm
@@ -47,11 +47,11 @@ Your participation is much appreciated.
47 47
   bioperl-l@bio.perl.org
48 48
 
49 49
 =head2 Support 
50  
- 
  50
+
51 51
 Please direct usage questions or support issues to the mailing list:
52  
-  
53  
-L<bioperl-l@bioperl.org>
54  
-  
  52
+
  53
+I<bioperl-l@bioperl.org>
  54
+
55 55
 rather than to the module maintainer directly. Many experienced and 
56 56
 reponsive experts will be able look at the problem and quickly 
57 57
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/AnnotationCollectionAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
+
53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
57 57
 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/BasePersistenceAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
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 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
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+I<bioperl-l@bioperl.org>
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 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/BiosequenceAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
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 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
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+I<bioperl-l@bioperl.org>
  56
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 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/PathAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
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 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
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+I<bioperl-l@bioperl.org>
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 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm
@@ -51,11 +51,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
51 51
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
52 52
 
53 53
 =head2 Support 
54  
- 
  54
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 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
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+I<bioperl-l@bioperl.org>
  58
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 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/Pg/TermAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
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53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
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 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/PrimarySeqAdaptor.pm
@@ -53,11 +53,11 @@ Your participation is much appreciated.
53 53
   bioperl-l@bio.perl.org
54 54
 
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 =head2 Support 
56  
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 Please direct usage questions or support issues to the mailing list:
58  
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59  
-L<bioperl-l@bioperl.org>
60  
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 rather than to the module maintainer directly. Many experienced and 
62 62
 reponsive experts will be able look at the problem and quickly 
63 63
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/ReferenceAdaptor.pm
@@ -51,11 +51,11 @@ Your participation is much appreciated.
51 51
   bioperl-l@bio.perl.org
52 52
 
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 =head2 Support 
54  
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  54
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 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
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+I<bioperl-l@bioperl.org>
  58
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 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/RelationshipAdaptor.pm
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47 47
   bioperl-l@bio.perl.org
48 48
 
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 =head2 Support 
50  
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  50
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 Please direct usage questions or support issues to the mailing list:
52  
-  
53  
-L<bioperl-l@bioperl.org>
54  
-  
  52
+
  53
+I<bioperl-l@bioperl.org>
  54
+
55 55
 rather than to the module maintainer directly. Many experienced and 
56 56
 reponsive experts will be able look at the problem and quickly 
57 57
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/SeqAdaptor.pm
@@ -52,11 +52,11 @@ Your participation is much appreciated.
52 52
   bioperl-l@bio.perl.org
53 53
 
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 =head2 Support 
55  
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  55
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 Please direct usage questions or support issues to the mailing list:
57  
-  
58  
-L<bioperl-l@bioperl.org>
59  
-  
  57
+
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  59
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60 60
 rather than to the module maintainer directly. Many experienced and 
61 61
 reponsive experts will be able look at the problem and quickly 
62 62
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/SeqFeatureAdaptor.pm
@@ -53,11 +53,11 @@ Your participation is much appreciated.
53 53
   bioperl-l@bio.perl.org
54 54
 
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 =head2 Support 
56  
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 Please direct usage questions or support issues to the mailing list:
58  
-  
59  
-L<bioperl-l@bioperl.org>
60  
-  
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 rather than to the module maintainer directly. Many experienced and 
62 62
 reponsive experts will be able look at the problem and quickly 
63 63
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/SimpleValueAdaptor.pm
@@ -45,11 +45,11 @@ Your participation is much appreciated.
45 45
   bioperl-l@bio.perl.org
46 46
 
47 47
 =head2 Support 
48  
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49 49
 Please direct usage questions or support issues to the mailing list:
50  
-  
51  
-L<bioperl-l@bioperl.org>
52  
-  
  50
+
  51
+I<bioperl-l@bioperl.org>
  52
+
53 53
 rather than to the module maintainer directly. Many experienced and 
54 54
 reponsive experts will be able look at the problem and quickly 
55 55
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/SpeciesAdaptor.pm
@@ -53,11 +53,11 @@ Your participation is much appreciated.
53 53
   bioperl-l@bio.perl.org
54 54
 
55 55
 =head2 Support 
56  
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 Please direct usage questions or support issues to the mailing list:
58  
-  
59  
-L<bioperl-l@bioperl.org>
60  
-  
  58
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  60
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 rather than to the module maintainer directly. Many experienced and 
62 62
 reponsive experts will be able look at the problem and quickly 
63 63
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/TermAdaptor.pm
@@ -46,11 +46,11 @@ Your participation is much appreciated.
46 46
   bioperl-l@bioperl.org
47 47
 
48 48
 =head2 Support 
49  
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  49
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50 50
 Please direct usage questions or support issues to the mailing list:
51  
-  
52  
-L<bioperl-l@bioperl.org>
53  
-  
  51
+
  52
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  53
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54 54
 rather than to the module maintainer directly. Many experienced and 
55 55
 reponsive experts will be able look at the problem and quickly 
56 56
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8  lib/Bio/DB/BioSQL/mysql/AnnotationCollectionAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/mysql/BasePersistenceAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
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 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/mysql/BiosequenceAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
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54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/mysql/PathAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
+
53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
  55
+I<bioperl-l@bioperl.org>
  56
+
57 57
 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/mysql/SpeciesAdaptorDriver.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
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54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/BioSQL/mysql/TermAdaptorDriver.pm
@@ -49,11 +49,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
49 49
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
50 50
 
51 51
 =head2 Support 
52  
- 
  52
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53 53
 Please direct usage questions or support issues to the mailing list:
54  
-  
55  
-L<bioperl-l@bioperl.org>
56  
-  
  54
+
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+I<bioperl-l@bioperl.org>
  56
+
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 rather than to the module maintainer directly. Many experienced and 
58 58
 reponsive experts will be able look at the problem and quickly 
59 59
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/CacheServer/SeqDB.pm
@@ -37,11 +37,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
37 37
   bioperl-l@bio.perl.org
38 38
 
39 39
 =head2 Support 
40  
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  40
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 Please direct usage questions or support issues to the mailing list:
42  
-  
43  
-L<bioperl-l@bioperl.org>
44  
-  
  42
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  44
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 rather than to the module maintainer directly. Many experienced and 
46 46
 reponsive experts will be able look at the problem and quickly 
47 47
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBAdaptorI.pm
@@ -53,11 +53,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
53 53
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
54 54
 
55 55
 =head2 Support 
56  
- 
  56
+
57 57
 Please direct usage questions or support issues to the mailing list:
58  
-  
59  
-L<bioperl-l@bioperl.org>
60  
-  
  58
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  59
+I<bioperl-l@bioperl.org>
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 rather than to the module maintainer directly. Many experienced and 
62 62
 reponsive experts will be able look at the problem and quickly 
63 63
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8  lib/Bio/DB/DBD.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI/Oracle.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI/Pg.pm
@@ -47,11 +47,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
47 47
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
48 48
 
49 49
 =head2 Support 
50  
- 
  50
+
51 51
 Please direct usage questions or support issues to the mailing list:
52  
-  
53  
-L<bioperl-l@bioperl.org>
54  
-  
  52
+
  53
+I<bioperl-l@bioperl.org>
  54
+
55 55
 rather than to the module maintainer directly. Many experienced and 
56 56
 reponsive experts will be able look at the problem and quickly 
57 57
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI/Transaction.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI/TransactionListener.pm
@@ -75,11 +75,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
75 75
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
76 76
 
77 77
 =head2 Support 
78  
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  78
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 Please direct usage questions or support issues to the mailing list:
80  
-  
81  
-L<bioperl-l@bioperl.org>
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 rather than to the module maintainer directly. Many experienced and 
84 84
 reponsive experts will be able look at the problem and quickly 
85 85
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8  lib/Bio/DB/DBI/base.pm
@@ -47,11 +47,11 @@ Bioperl mailing list.  Your participation is much appreciated.
47 47
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
48 48
 
49 49
 =head2 Support 
50  
- 
  50
+
51 51
 Please direct usage questions or support issues to the mailing list:
52  
-  
53  
-L<bioperl-l@bioperl.org>
54  
-  
  52
+
  53
+I<bioperl-l@bioperl.org>
  54
+
55 55
 rather than to the module maintainer directly. Many experienced and 
56 56
 reponsive experts will be able look at the problem and quickly 
57 57
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/DBI/mysql.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
+
  56
+I<bioperl-l@bioperl.org>
  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/PersistenceAdaptorI.pm
@@ -54,11 +54,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
54 54
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
55 55
 
56 56
 =head2 Support 
57  
- 
  57
+
58 58
 Please direct usage questions or support issues to the mailing list:
59  
-  
60  
-L<bioperl-l@bioperl.org>
61  
-  
  59
+
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62 62
 rather than to the module maintainer directly. Many experienced and 
63 63
 reponsive experts will be able look at the problem and quickly 
64 64
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8  lib/Bio/DB/Persistent/BioNamespace.pm
@@ -36,11 +36,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
36 36
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
37 37
 
38 38
 =head2 Support 
39  
- 
  39
+
40 40
 Please direct usage questions or support issues to the mailing list:
41  
-  
42  
-L<bioperl-l@bioperl.org>
43  
-  
  41
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44 44
 rather than to the module maintainer directly. Many experienced and 
45 45
 reponsive experts will be able look at the problem and quickly 
46 46
 address it. Please include a thorough description of the problem 
8  lib/Bio/DB/Persistent/ObjectRelMapperI.pm
@@ -50,11 +50,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
50 50
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
51 51
 
52 52
 =head2 Support 
53  
- 
  53
+
54 54
 Please direct usage questions or support issues to the mailing list:
55  
-  
56  
-L<bioperl-l@bioperl.org>
57  
-  
  55
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  57
+
58 58
 rather than to the module maintainer directly. Many experienced and 
59 59
 reponsive experts will be able look at the problem and quickly 
60 60
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8  lib/Bio/DB/Persistent/PersistentObject.pm
@@ -74,11 +74,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
74 74
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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 =head2 Support 
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