cosmetic: make it explicit that we are importing rearrange() and throw()

modules/Bio/EnsEMBL/Hive/Accumulator.pm

@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::Accumulator;
 use strict;
 use Scalar::Util ('weaken');
 
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 sub new {
     my $class = shift @_;

modules/Bio/EnsEMBL/Hive/Analysis.pm

@@ -24,7 +24,8 @@
 package Bio::EnsEMBL::Hive::Analysis;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 use base (  'Bio::EnsEMBL::Storable',       # inherit dbID(), adaptor() and new() methods
          );

modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm

@@ -44,10 +44,11 @@ package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
 use strict;
 use Scalar::Util ('weaken');
 
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use Bio::EnsEMBL::Utils::Exception ('throw');
+
 use Bio::EnsEMBL::Hive::URLFactory;
 use Bio::EnsEMBL::Hive::Extensions;
-use Bio::EnsEMBL::Utils::Argument;
-use Bio::EnsEMBL::Utils::Exception;
 
 =head2 new
 

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -27,7 +27,8 @@
 package Bio::EnsEMBL::Hive::AnalysisJob;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 use Bio::EnsEMBL::Hive::Utils ('destringify');
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;

modules/Bio/EnsEMBL/Hive/AnalysisStats.pm

@@ -28,7 +28,8 @@ package Bio::EnsEMBL::Hive::AnalysisStats;
 use strict;
 use Scalar::Util ('weaken');
 
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+
 use Bio::EnsEMBL::Hive::Analysis;
 
 

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

@@ -40,8 +40,6 @@
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw);
 
 use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 

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

@@ -40,11 +40,11 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 
 use strict;
 
-use Bio::EnsEMBL::Utils::Argument;
-use Bio::EnsEMBL::Utils::Exception;
-use Bio::EnsEMBL::Hive::Worker;
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use Bio::EnsEMBL::Utils::Exception ('throw');
+
+use Bio::EnsEMBL::Hive::Utils ('stringify');
 use Bio::EnsEMBL::Hive::AnalysisJob;
-use Bio::EnsEMBL::Hive::Utils 'stringify';  # import 'stringify()'
 
 use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 

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

@@ -40,9 +40,9 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
 
 use strict;
 
-use Bio::EnsEMBL::Hive::AnalysisStats;
 use Bio::EnsEMBL::Utils::Argument;
-use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Utils::Exception ('throw');
+use Bio::EnsEMBL::Hive::AnalysisStats;
 
 use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 

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

@@ -36,7 +36,9 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
 package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument;
+
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+
 use Bio::EnsEMBL::Hive::URLFactory;
 use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
 

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

@@ -24,8 +24,8 @@
 package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
 
 use strict;
+use Bio::EnsEMBL::Hive::Utils ('stringify');
 use Bio::EnsEMBL::Hive::DataflowRule;
-use Bio::EnsEMBL::Hive::Utils ('stringify');  # import 'stringify()'
 
 use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
 

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

@@ -10,7 +10,7 @@
 
 =head1 DESCRIPTION
 
-  This module extends EnsEMBL Core's MetaContainer, adding some Hive-specific stuff.
+  This module extends EnsEMBL Core's BaseMetaContainer, adding some Hive-specific stuff.
 
 =head1 CONTACT
 
@@ -22,7 +22,7 @@
 package Bio::EnsEMBL::Hive::DBSQL::MetaContainer;
 
 use strict;
-use Bio::EnsEMBL::Hive::Utils ('destringify');  # import both functions
+use Bio::EnsEMBL::Hive::Utils ('destringify');
 
 use base ('Bio::EnsEMBL::DBSQL::BaseMetaContainer');
 

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -50,10 +50,11 @@
 package Bio::EnsEMBL::Hive::DataflowRule;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
-use Bio::EnsEMBL::Utils::Exception;
 
-use Bio::EnsEMBL::Hive::Utils ('stringify');  # import 'stringify()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use Bio::EnsEMBL::Utils::Exception ('throw');
+
+use Bio::EnsEMBL::Hive::Utils ('stringify');
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
 
 use base (  'Bio::EnsEMBL::Storable',       # inherit dbID(), adaptor() and new() methods

modules/Bio/EnsEMBL/Hive/NakedTable.pm

@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::NakedTable;
 use strict;
 use Scalar::Util ('weaken');
 
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 sub new {
     my $class = shift @_;

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -48,8 +48,9 @@ package Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 use strict;
 use warnings;
 
-use Bio::EnsEMBL::Utils::Argument;          # import 'rearrange()'
-use Bio::EnsEMBL::Hive::Utils 'stringify';  # import 'stringify()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
+
+use Bio::EnsEMBL::Hive::Utils ('stringify');
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 use Bio::EnsEMBL::Hive::Analysis;

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -86,9 +86,11 @@ package Bio::EnsEMBL::Hive::Process;
 
 use strict;
 use warnings;
+
 use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::Utils::Argument;
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 use Bio::EnsEMBL::Utils::Exception ('throw');
+
 use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
 use Bio::EnsEMBL::Hive::Utils ('stringify', 'go_figure_dbc');
 use Bio::EnsEMBL::Hive::Utils::Stopwatch;

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -63,10 +63,9 @@ use strict;
 use POSIX;
 use File::Path 'make_path';
 
-use Bio::EnsEMBL::Utils::Argument;
-use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
-use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash');  # import 'destringify()' and 'dir_revhash()'
+use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash');  # NB: needed by invisible code
 use Bio::EnsEMBL::Hive::AnalysisJob;
 use Bio::EnsEMBL::Hive::Worker;
 

modules/Bio/EnsEMBL/Hive/ResourceClass.pm

@@ -26,7 +26,8 @@
 package Bio::EnsEMBL::Hive::ResourceClass;
 
 use strict;
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 use base (  'Bio::EnsEMBL::Storable',       # inherit dbID(), adaptor() and new() methods
          );

modules/Bio/EnsEMBL/Hive/ResourceDescription.pm

@@ -28,7 +28,7 @@ package Bio::EnsEMBL::Hive::ResourceDescription;
 use strict;
 use Scalar::Util ('weaken');
 
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 sub new {
     my $class = shift @_;

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -66,8 +66,7 @@ package Bio::EnsEMBL::Hive::Worker;
 use strict;
 use POSIX;
 
-use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
-use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Utils::Argument ('rearrange');
 
 use Bio::EnsEMBL::Hive::Analysis;
 use Bio::EnsEMBL::Hive::AnalysisStats;