Commit 59414cf7 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

POD corrections

parent 375bccae
......@@ -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
......
......@@ -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.
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
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