Commit 9901314d authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Correct documentation.

parent 73efbf7d
......@@ -87,7 +87,7 @@ sub new {
=head2 fetch_all
Args : none
Example : my @analysis = $analysis_adaptor->fetch_all()
Example : my @analysis = @{$analysis_adaptor->fetch_all()};
Description: fetches all of the Analysis objects from the database and caches
them internally.
Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
......
......@@ -55,8 +55,9 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
A lower bound for the hcoverage of feats to obtain.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats =
$adaptor->fetch_all_by_Slice_and_hcoverage( $slice, 50.0 );
Example : @feats = @{
$adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
50.0 ) };
Description: Returns a listref of features created from the
database which are on the Slice $slice and with a
hcoverage greater than $hcoverage. If logic name
......@@ -92,8 +93,9 @@ sub fetch_all_by_Slice_and_hcoverage {
should be restricted.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats =
$adaptor->fetch_all_by_Slice_and_external_db( $slice, 'EMBL' );
Example : @feats = @{
$adaptor->fetch_all_by_Slice_and_external_db( $slice,
'EMBL' ) };
Description: Returns a listref of features created from the
database which are on the Slice $slice and associated
with external DB $external_db_name. If logic name
......@@ -151,7 +153,8 @@ sub fetch_all_by_Slice_and_external_db {
to obtain.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats = $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 );
Example : @feats =
@{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
Description: Returns a listref of features created from the
database which are on the Slice $slice and with a
percentage identity greater than $pid. If logic name
......@@ -197,7 +200,8 @@ sub fetch_all_by_Slice_and_pid {
The analysis logic name of the type of features to
obtain.
Example : @feats =
$adaptor->fetch_all_by_hit_name( $name, $logic_name );
@{ $adaptor->fetch_all_by_hit_name( $name,
$logic_name ); }
Description: Returns a listref of features created from the
database which correspond to the given hit_name. If
logic name is defined, only features with an analysis
......@@ -244,7 +248,8 @@ sub fetch_all_by_hit_name {
The analysis logic name of the type of features to
obtain.
Example : @feats =
$adaptor->fetch_all_by_hit_name( $name, $logic_name );
@{ $adaptor->fetch_all_by_hit_name( $name,
$logic_name ) };
Description: Returns a listref of features created from the
database which start with the given hit_name. If
logic name is defined, only features with an analysis
......
......@@ -89,7 +89,7 @@ sub get_schema_version {
Arg [1] : string $key
the key to obtain values from the meta table with
Example : my @values = $meta_container->list_value_by_key($key);
Example : my @values = @{ $meta_container->list_value_by_key($key) };
Description: gets a value for a key. Can be anything
Returntype : listref of strings
Exceptions : none
......
......@@ -359,7 +359,7 @@ sub fetch_by_exon_stable_id {
Arg [1] : String $domain
The domain to fetch genes from
Example : my @genes = $gene_adaptor->fetch_all_by_domain($domain);
Example : my @genes = @{ $gene_adaptor->fetch_all_by_domain($domain) };
Description: Retrieves a listref of genes whose translation contain interpro
domain $domain. The genes are returned in their native coord
system (i.e. the coord_system they are stored in). If the coord
......@@ -1343,7 +1343,9 @@ sub remove {
Arg [1] : String $gene_stable_id
The stable ID of the gene to obtain
Example : @i = $gene_adaptor->get_Interpro_by_geneid($gene->stable_id());
Example : @i = @{
$gene_adaptor->get_Interpro_by_geneid(
$gene->stable_id() ) };
Description: Gets interpro accession numbers by gene stable id. A hack really
- we should have a much more structured system than this.
Returntype : listref of strings (Interpro_acc:description)
......
......@@ -61,7 +61,8 @@ use vars qw(@ISA);
Arg [1] : int $transl
the internal id of the translation corresponding to protein
whose features are desired
Example : @prot_feats = $prot_feat_adaptor->fetch_by_translation_id(1234);
Example : @prot_feats =
@{ $prot_feat_adaptor->fetch_by_translation_id(1234) };
Description: Gets all protein features present on a peptide using the
translations internal identifier. This method will return
an unsorted list of all protein_feature types. The feature
......
......@@ -338,8 +338,11 @@ sub get {
Arg[1] : String $dbtype - db type ('source' or 'target')
Arg[2] : String $class - key identifying a gene type (see class_key())
Arg[3] : String $subclass - status identifier (e.g. 'mapped', 'lost')
Example : my @mapped_stable_ids = $analyser->get_all_by_subclass('source',
'KNOWN-ensembl-protein_coding', 'mapped');
Example : my @mapped_stable_ids = @{
$analyser->get_all_by_subclass(
'source', 'KNOWN-ensembl-protein_coding',
'mapped'
) };
Description : Gets a list of stable Id for a given subclass.
Return type : Arrayref of String (stable Ids)
Exceptions : thrown on missing arguments
......@@ -365,8 +368,9 @@ sub get_all_by_subclass {
Arg[1] : String $dbtype - db type ('source' or 'target')
Arg[2] : String $class - key identifying a gene type (see class_key())
Example : my @stable_ids = $analyser->get_all_by_class('source',
'KNOWN-ensembl-protein_coding');
Example : my @stable_ids = @{
$analyser->get_all_by_class( 'source',
'KNOWN-ensembl-protein_coding' ) };
Description : Gets a list of stable Id for a given class.
Return type : Arrayref of String (stable Ids)
Exceptions : thrown on missing arguments
......
......@@ -379,7 +379,7 @@ sub get_score {
=head2 get_targets_for_source
Arg[1] : Int $source - source object's internal Id ("dbID")
Example : my @targets = $gene_scores->get_targets_for_source(1234);
Example : my @targets = @{ $gene_scores->get_targets_for_source(1234) };
Description : Returns a list of all targets which have a score against a given
source object.
Return type : Arrayref of Int (target objects' internal Ids)
......@@ -401,7 +401,7 @@ sub get_targets_for_source {
=head2 get_Entries_for_source
Arg[1] : Int $source - source object's internal Id ("dbID")
Example : my @entries = $gene_scores->get_Entries_for_source(1234);
Example : my @entries = @{ $gene_scores->get_Entries_for_source(1234) };
Description : Returns a list of all Entries in the scoring matrix for a given
source object.
Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
......@@ -424,7 +424,7 @@ sub get_Entries_for_source {
=head2 get_sources_for_target
Arg[1] : Int $target - target object's internal Id ("dbID")
Example : my @sources = $gene_scores->get_sources_for_target(5678);
Example : my @sources = @{ $gene_scores->get_sources_for_target(5678) };
Description : Returns a list of all sources which have a score against a given
target object.
Return type : Arrayref of Int (source objects' internal Ids)
......@@ -446,7 +446,7 @@ sub get_sources_for_target {
=head2 get_Entries_for_target
Arg[1] : Int $target - target object's internal Id ("dbID")
Example : my @entries = $gene_scores->get_Entries_for_target(5678);
Example : my @entries = @{ $gene_scores->get_Entries_for_target(5678) };
Description : Returns a list of all Entries in the scoring matrix for a given
target object.
Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
......
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