bulk fixing of PODs - may have accidentally broken something?

modules/Bio/EnsEMBL/Hive.pm

@@ -49,11 +49,9 @@
   It is also responsible for interfacing with the Queen to identify workers which died
   unexpectantly so that she can free the dead workers unfinished jobs.
 
-
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 

modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod 
 
 =head1 NAME
 
@@ -28,8 +28,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -39,8 +38,6 @@
 =cut
 
 
-# Let the code begin...
-
 
 package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
 

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

 #
 # You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
 
 =pod 
 
@@ -16,8 +14,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -26,6 +23,7 @@
 
 =cut
 
+
 package Bio::EnsEMBL::Hive::AnalysisJob;
 
 use strict;

modules/Bio/EnsEMBL/Hive/AnalysisStats.pm

 #
 # You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
 
 =pod 
 
 =head1 NAME
+
   Bio::EnsEMBL::Hive::AnalysisStats
 
 =head1 SYNOPSIS
@@ -13,14 +12,17 @@
 =head1 DESCRIPTION
 
 =head1 CONTACT
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
+
   The rest of the documentation details each of the object methods.
   Internal methods are usually preceded with a _
+
 =cut
 
+
 package Bio::EnsEMBL::Hive::AnalysisStats;
 
 use strict;

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
 
@@ -25,8 +25,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -36,8 +35,6 @@
 =cut
 
 
-# Let the code begin...
-
 
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
 

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm

@@ -7,33 +7,35 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
+
   Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
 
 =head1 SYNOPSIS
+
   $dataDBA = $db_adaptor->get_AnalysisDataAdaptor;
 
 =head1 DESCRIPTION
+
    analysis_data table holds LONGTEXT data for use by the analysis system.
    This data is general purpose and it's up to each analysis to
    determine how to use it.
    This Adaptor module is used to access/store this data.
 
 =head1 CONTACT
-  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
+
   The rest of the documentation details each of the object methods.
   Internal methods are preceded with a _
 
 =cut
 
 
-# Let the code begin...
-
 
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
 

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
 
@@ -25,8 +25,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -36,7 +35,6 @@
 =cut
 
 
-# Let the code begin...
 
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm

@@ -7,31 +7,34 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
+
   Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor
 
 =head1 SYNOPSIS
+
   $analysisStatsAdaptor = $db_adaptor->get_AnalysisStatsAdaptor;
   $analysisStatsAdaptor = $analysisStats->adaptor;
 
 =head1 DESCRIPTION
+
   Module to encapsulate all db access for persistent class AnalysisStats.
   There should be just one per application and database connection.
 
 =head1 CONTACT
-  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
+
   The rest of the documentation details each of the object methods.
   Internal methods are usually preceded with a _
 
 =cut
 
 
-# Let the code begin...
 
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
 

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
 
@@ -22,20 +22,17 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
         -driver => 'mysql',
         );
 
-
 =head1 DESCRIPTION
+
   This object represents the handle for a Hive system enabled database
 
 =head1 CONTACT
 
-Post questions the the EnsEMBL developer list: <ensembl-dev@ebi.ac.uk>
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =cut
 
 
-# Let the code begin...
-
-
 package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 
 use vars qw(@ISA);

modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
 
@@ -25,8 +25,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -36,9 +35,6 @@
 =cut
 
 
-# Let the code begin...
-
-
 package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
 
 use strict;

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -7,7 +7,7 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod
 
 =head1 NAME
 
@@ -25,11 +25,9 @@
   be specified with a network savy URL like
   mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
 
-
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -39,9 +37,6 @@
 =cut
 
 
-# Let the code begin...
-
-
 package Bio::EnsEMBL::Hive::DataflowRule;
 
 use strict;

modules/Bio/EnsEMBL/Hive/Extensions.pm

@@ -9,24 +9,15 @@
 
   Bio::EnsEMBL::Hive::Extensions
 
-=cut
-
 =head1 SYNOPSIS
 
   Object categories to extend the functionality of existing classes
 
-=cut
-
 =head1 DESCRIPTION
 
-=cut
-
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
-
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -35,6 +26,7 @@
 
 =cut
 
+
 use strict;
 
 use Bio::EnsEMBL::Utils::Exception;

modules/Bio/EnsEMBL/Hive/Process.pm

 # You may distribute this module under the same terms as perl itself #
-# POD documentation - main docs before the code
 
 =pod 
 
@@ -7,8 +6,6 @@
 
   Bio::EnsEMBL::Hive::Process
 
-=cut
-
 =head1 SYNOPSIS
 
   Abstract superclass.  Each Process makes up the individual building blocks 
@@ -73,14 +70,9 @@
      http://en.wikipedia.org/wiki/Emergence
   
 
-=cut
-
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
-
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -89,6 +81,8 @@
 
 =cut
 
+
+
 my $g_hive_process_workdir;  # a global directory location for the process using this module
 
 package Bio::EnsEMBL::Hive::Process;

modules/Bio/EnsEMBL/Hive/Queen.pm

 #
 # You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
 
 =pod 
 
@@ -49,8 +47,7 @@
 
 =head1 CONTACT
 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -59,6 +56,7 @@
 
 =cut
 
+
 package Bio::EnsEMBL::Hive::Queen;
 
 use strict;

modules/Bio/EnsEMBL/Hive/RunnableDB/Dummy.pm

@@ -9,8 +9,6 @@
 
 Bio::EnsEMBL::Hive::RunnableDB::Dummy
 
-=cut
-
 =head1 SYNOPSIS
 
 my $db      = Bio::EnsEMBL::DBAdaptor->new($locator);
@@ -23,8 +21,6 @@ $repmask->run();
 $repmask->output();
 $repmask->write_output(); #writes to DB
 
-=cut
-
 =head1 DESCRIPTION
 
 This object is used as a place holder in the hive system.
@@ -32,13 +28,9 @@ It does nothing, but is needed so that a Worker can grab
 a job, pass the input through to output, and create the
 next layer of jobs in the system.
 
-=cut
-
 =head1 CONTACT
 
-jessica@ebi.ac.uk
-
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 

modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm

@@ -9,8 +9,6 @@
 
 Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
 
-=cut
-
 =head1 SYNOPSIS
 
 my $db      = Bio::EnsEMBL::DBAdaptor->new($locator);
@@ -23,20 +21,14 @@ $runDB->run();
 $runDB->output();
 $runDB->write_output(); #writes to DB
 
-=cut
-
 =head1 DESCRIPTION
 
 This object is a very simple module.  It takes the input_id
 and runs it as a system command.
 
-=cut
-
 =head1 CONTACT
 
-jessica@ebi.ac.uk
-
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -45,6 +37,7 @@ Internal methods are usually preceded with a _
 
 =cut
 
+
 package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
 
 use strict;

modules/Bio/EnsEMBL/Hive/RunnableDB/Test.pm

@@ -9,8 +9,6 @@
 
 Bio::EnsEMBL::Hive::RunnableDB::Test
 
-=cut
-
 =head1 SYNOPSIS
 
 my $db      = Bio::EnsEMBL::DBAdaptor->new($locator);
@@ -23,8 +21,6 @@ $repmask->run();
 $repmask->output();
 $repmask->write_output(); #writes to DB
 
-=cut
-
 =head1 DESCRIPTION
 
 This object is used to test failure of jobs in the hive system.
@@ -35,13 +31,9 @@ It parses the analysis.parameters and analysis_job.input_id as
 (string representing) hasrefs and extracts the divisor and the value.
 If the modulo (value % divisor) is 0, the job will fail.
 
-=cut
-
 =head1 CONTACT
 
-ensembl-dev@ebi.ac.uk
-
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
 
@@ -50,6 +42,8 @@ Internal methods are usually preceded with a _
 
 =cut
 
+
+
 package Bio::EnsEMBL::Hive::RunnableDB::Test;
 
 use strict;

modules/Bio/EnsEMBL/Hive/URLFactory.pm

@@ -7,30 +7,33 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
+=pod 
 
 =head1 NAME
+
   Bio::EnsEMBL::Hive::URLFactory
 
 =head1 SYNOPSIS
+
   $someObj = Bio::EnsEMBL::Hive::URLFactory->fetch($url_string);
   Bio::EnsEMBL::Hive::URLFactory->store($object);
 
 =head1 DESCRIPTION  
+
   Module to parse URL strings and return EnsEMBL objects be them
   DBConnections, DBAdaptors, or specifics like Analysis, Member, Gene, ....
 
 =head1 CONTACT
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX
+
   The rest of the documentation details each of the object methods.
   Internal methods are usually preceded with a _
-=cut
 
+=cut
 
-# Let the code begin...
 
 # global instance to cache connection to limit the number of open DB connections
 my $_URLFactory_global_instance;

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -9,8 +9,6 @@
 
   Bio::EnsEMBL::Hive::Worker
 
-=cut
-
 =head1 DESCRIPTION
 
   Object which encapsulates the details of how to find jobs, how to run those
@@ -51,14 +49,9 @@
   It is also responsible for interfacing with the Queen to identify workers which died
   unexpectantly so that she can free the dead workers unfinished jobs.
 
-=cut
-
 =head1 CONTACT
- 
-  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
-  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
 
-=cut
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =head1 APPENDIX