POD corrections

modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm

@@ -22,10 +22,6 @@
 
 Bio::EnsEMBL::DBFile::FileAdaptor - Base Adaptor for direct file access
 
-=head1 SYNOPSIS
-
-
-
 =head1 DESCRIPTION
 
 Basic wrapper class to provide access to file based data.
@@ -38,9 +34,6 @@ the required amount of data covering the slice.
 Currently only works as hybrid DBAdaptor e.g. ResultFeatureAdaptor which inherits both from 
 here and BaseFeatureAdaptor.
 
-=head1 SEE ALSO
-
-
 =cut
 
 
@@ -102,9 +95,9 @@ sub get_filehandle{
 
   Arg[1]     : string     - filepath
   Arg[2]     : HASHREF    - Optional params:
-                                 -binmode       => 0|1,   # Boolean i.e. treat file as binary
-                                 -file_operator => '>'    # Default is '<'
-                                #-perms_octal   =>  # Requires FileHandle
+                          -binmode       => 0|1,   # Boolean i.e. treat file as binary
+                          -file_operator => '>'    # Default is '<'
+                         #-perms_octal   =>  # Requires FileHandle
   Example    : my $fh     = $self->open_file($filepath, {-binmode = > 1, -file_operator => '>'});
   Description: Opens a file for reading or writing.
   Returntype : GLOB/undef - filehandle

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

@@ -554,7 +554,7 @@ sub fetch_by_dbID {
   Arg [1]    : none
   Example    : $cs = $csa->fetch_top_level();
   Description: Retrieves the toplevel pseudo coordinate system.
-  Returntype : a Bio::EnsEMBL::CoordSystem object
+  Returntype : Bio::EnsEMBL::CoordSystem object
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -758,7 +758,7 @@ sub get_mapping_path {
 
   Arg [1]    : Bio::EnsEMBL::CoordSystem $cs1
   Arg [2]    : Bio::EnsEMBL::CoordSystem $cs2
-  Arg [3..n] : Bio::EnsEMBL::CoordSystems $cs3..$csN
+  Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
   Example    : my $pathref = $csa->store_mapping_path($cs1,$cs2);
   Description: Given two or more coordinate systems this will store 
                mapping paths between them in the database. 

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -92,7 +92,7 @@ my $reg = "Bio::EnsEMBL::Registry";
                 -driver => 'mysql'
               );
 
-  Example2   : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+              $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
                 -species => 'Homo_sapiens',
                 -group   => 'core',
                 -user    => 'root',
@@ -101,7 +101,7 @@ my $reg = "Bio::EnsEMBL::Registry";
                 -driver  => 'mysql'
               );
 
-  Example3   : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+              $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
                 -species         => 'staphylococcus_aureus',
                 -group           => 'core',
                 -user            => 'root',
@@ -563,7 +563,7 @@ sub get_adaptor {
 =head2 set_adaptor
 
   Arg [1]    : Canonical data type for new adaptor.
-	Arg [2]    : Object defining the adaptor for arg1.
+  Arg [2]    : Object defining the adaptor for arg1.
   Example    : $aa = Bio::EnsEMBL::DBSQL::GeneAdaptor->new($db_adaptor);
              : $db_adaptor->set_adaptor("Gene", $ga)
   Description: Stores the object which represents the adaptor for the

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -905,7 +905,7 @@ sub quote_identifier {
                disconect_when_inactive flag is set.
                Users may call it whenever they want to disconnect. Connection will
                reestablish on next access to db_handle()
-  Returntype : 0,1
+  Returntype : 1 or 0
                1=problem trying to disconnect while a statement handle was still active
   Exceptions : none
   Caller     : Bio::EnsEMBL::DBSQL::SQL::StatementHandle::DESTROY

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -1731,7 +1731,7 @@ SQL
   Arg [3]    : (optional) string $extraType
   	       other object type to be returned
   Example    : $self->_type_by_external_db_id(1030, 'Translation');
-  Description: Gets
+  Description: Gets.
                NOTE:  In a multi-species database, this method will
                return all the entries matching the search criteria, not
                just the ones associated with the current species.
@@ -1739,7 +1739,7 @@ SQL
   Exceptions : none
   Caller     : list_translation_ids_by_extids
                translationids_by_extids
-  	       geneids_by_extids
+  	           geneids_by_extids
   Status     : Stable
 
 =cut
@@ -2065,7 +2065,7 @@ sub geneids_by_extids{
 
 =head2 translationids_by_extids
 
-  Description:  DEPRECATED use list_translation_ids_by_extids instead
+  DEPRECATED use list_translation_ids_by_extids instead
 
 =cut
 
@@ -2078,7 +2078,7 @@ sub translationids_by_extids{
 
 =head2 transcriptids_by_extids
 
-  Description: DEPRECATED use transcriptids_by_extids instead
+  DEPRECATED use transcriptids_by_extids instead
 
 =cut
 

modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm

@@ -62,7 +62,7 @@ my $GLOBAL_BASE_PATH;
 =head2 global_base_path
 
   Arg[1]     	: String; base path 
-  Example			: Bio::EnsEMBL::DBSQL::DataFileAdaptor->global_base_path('/base/path');
+  Example       : Bio::EnsEMBL::DBSQL::DataFileAdaptor->global_base_path('/base/path');
   Description	: Stores a global value to be used when building data file paths
   Returntype 	: String
   Exceptions 	: None
@@ -101,12 +101,12 @@ sub get_base_path {
 
 =head2 DataFile_to_extension
 
+  Deprecated
   Arg[1]      : Bio::EnsEMBL::DataFile
   Example     : my $ext = $dfa->DataFile_to_extension($bam_df);
   Description : Returns an expected extension for the given DataFile type
   Returntype  : Scalar of the expected file extension
   Exceptions  : Raised if the given file type is not understood
-  Status      : Deprecated
 
 =cut
 
@@ -144,12 +144,12 @@ sub DataFile_to_extensions {
 
 =head2 DataFile_to_adaptor
 
-  Arg[1]     	: Bio::EnsEMBL::DataFile
-  Arg[2]      : (optional) base path
-  Example			: my $bam = $dfa->DataFile_to_adaptor($bam_df);
-  Description	: Returns an adaptor instance which will access the given DataFile
-  Returntype 	: Scalar actual return depends upon the given file type
-  Exceptions 	: Raised if the given file type is not understood
+  Arg[1]        : Bio::EnsEMBL::DataFile
+  Arg[2]        : (optional) base path
+  Example       : my $bam = $dfa->DataFile_to_adaptor($bam_df);
+  Description   : Returns an adaptor instance which will access the given DataFile
+  Returntype    : Scalar actual return depends upon the given file type
+  Exceptions    : Raised if the given file type is not understood
 
 =cut
 
@@ -181,7 +181,7 @@ sub DataFile_to_adaptor {
 =head2 fetch_all_by_logic_name
 
   Args [1]   	: String $logic_name for the linked analysis 
-  Example			: my $dfs = $dfa->fetch_all_by_logic_name('bam_alignments');
+  Example       : my $dfs = $dfa->fetch_all_by_logic_name('bam_alignments');
   Description	: Returns all DataFile entries linked to the given analysis 
                 logic name
   Returntype 	: ArrayRef contains Bio::EnsEMBL::DataFile instances

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -935,7 +935,7 @@ sub fetch_all_by_GOTerm_accession {
                The gene to fetch alternative alleles for
   Example    : my @alt_genes = @{ $gene_adaptor->fetch_all_alt_alleles($gene) };
                foreach my $alt_gene (@alt_genes) {
-                 print "Alternate allele: " . $alt_gene->stable_id() . "\n";
+                 print "Alternate allele: " . $alt_gene->stable_id() . "\n" ;
                }
   Description: Retrieves genes which are alternate alleles to a provided gene.
                Alternate alleles in Ensembl are genes which are similar and are
@@ -2193,7 +2193,7 @@ sub fetch_nearest_Gene_by_Feature{
 
 =head2 fetch_by_maximum_DBLink
 
- Description: DEPRECATED - use fetch_all_by_external_name instead
+ DEPRECATED - use fetch_all_by_external_name instead
 
 =cut
 
@@ -2223,7 +2223,7 @@ sub fetch_by_maximum_DBLink {
 
 =head2 get_display_xref
 
-  Description: DEPRECATED use $gene->display_xref
+  DEPRECATED use $gene->display_xref
 
 =cut
 
@@ -2269,7 +2269,7 @@ sub get_display_xref {
 
 =head2 get_description
 
-  Description: DEPRECATED, use gene->get_description
+  DEPRECATED, use gene->get_description
 
 =cut
 
@@ -2296,7 +2296,7 @@ sub get_description {
 
 =head2 fetch_by_Peptide_id
 
-  Description: DEPRECATED, use fetch_by_translation_stable_id()
+  DEPRECATED, use fetch_by_translation_stable_id()
 
 =cut
 
@@ -2312,7 +2312,7 @@ sub fetch_by_Peptide_id {
 
 =head2 get_stable_entry_info
 
-  Description: DEPRECATED use $gene->stable_id instead
+  DEPRECATED use $gene->stable_id instead
 
 =cut
 
@@ -2349,7 +2349,7 @@ sub get_stable_entry_info {
 
 =head2 fetch_all_by_DBEntry
 
-  Description: DEPRECATED - Use fetch_all_by_external_name instead
+  DEPRECATED - Use fetch_all_by_external_name instead
 
 =cut