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Commit a8bfbd14 authored by Arne Stabenau's avatar Arne Stabenau
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podding while test writing

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modules/Bio/EnsEMBL/Gene.pm
+ 174
− 118
View file @ a8bfbd14
......@@ -66,17 +66,6 @@ sub new {
}
=head2 start
Title : start
Usage : $start = $gene->start()
Function : Gets/Sets the lowest start coordinate of this genes exons.
No consistancy check is performed and if this
is used as a setter and potentially the start could be set to
a value which does not correspond to the lowest exon start.
Returns : int
Args : none, or the start coordinate of this gene
=cut
=head2 start
......@@ -260,6 +249,18 @@ sub chr_name {
}
=head2 source
Arg [1] : string $source
Example : none
Description: get/set for attribute source
Returntype : string
Exceptions : none
Caller : general
=cut
sub source {
my ($self, $source) = @_;
......@@ -271,18 +272,20 @@ sub source {
}
=head2 is_known
Title : is_known
Usage : if( $gene->is_known )
Function: returns true if there are any dblinks on the gene or
transcript objects
Example :
Returns :
Args :
Args : none
Example : none
Description: returns true if the Gene or one of its Transcripts have
DBLinks
Returntype : 0,1
Exceptions : none
Caller : general
=cut
sub is_known{
my ($self) = @_;
my @array;
......@@ -303,15 +306,16 @@ sub is_known{
=head2 adaptor
Title : adaptor
Usage :
Function: give this genes GeneAdaptor if known
Example :
Returns :
Args :
Arg [1] : Bio::EnsEMBL::DBSQL::GeneAdaptor $adaptor
Example : none
Description: get/set for attribute adaptor
Returntype : Bio::EnsEMBL::DBSQL::GeneAdaptor
Exceptions : none
Caller : set only used by adaptor on store or retrieve
=cut
sub adaptor {
my ($self, $arg) = @_;
......@@ -323,16 +327,19 @@ sub adaptor {
=head2 analysis
Title : analysis
Usage : $gene->analysis($analysisObject)
Function: get/set this genes analysis object
Returns : on get the analysis object
Args : newvalue (optional)
Arg [1] : Bio::EnsEMBL::Analysis $analysis
Example : none
Description: get/set for attribute analysis
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
=cut
sub analysis {
my ($self,$value) = @_;
if( defined $value ) {
......@@ -343,17 +350,19 @@ sub analysis {
=head2 dbID
Title : dbID
Usage : $id = $obj->dbID();
Function: internal db id if available
Example :
Returns :
Args :
Arg [1] : int $dbID
Example : none
Description: get/set for attribute dbID
Returntype : int
Exceptions : none
Caller : set only by adaptor on store or retrieve
=cut
sub dbID {
my ($self, $arg) = @_;
......@@ -367,12 +376,14 @@ sub dbID {
=head2 external_name
Title : external_name
Usage : $ext_name = $obj->external_name();
Function: external_name if available
Example :
Returns : the external name of this gene
Args : new external name (optional)
Arg [1] : string $external_name
Example : none
Description: get/set for attribute external_name. It could be calculated
from dblinks in a species dependent way. Well introduce
that later.
Returntype : string
Exceptions : none
Caller : Lite::GeneAdaptor knows how to set it correct
=cut
......@@ -386,6 +397,21 @@ sub external_name {
return $self->{'_external_name'};
}
=head2 external_db
Arg [1] : string $external_db
Example : none
Description: get/set for attribute external_db. The db is the one that
belongs to the external_name
Returntype : string
Exceptions : none
Caller : general
=cut
sub external_db {
my ($self, $arg ) = @_;
......@@ -398,20 +424,28 @@ sub external_db {
=head2 description
Title : description
Usage : $gene->description
Function: gets the gene description line. Setting is not allowed
Example :
Returns : a string
Args : none
Arg [1] : (optional) string $description
Example : none
Description: you can set get this argument. If not set its lazy loaded
from attached adaptor.
Returntype : string
Exceptions : if no GeneAdaptor is set and no description is there
Caller : general
=cut
sub description {
my ($self) = @_;
my ($self, $arg) = @_;
if( defined $arg ) {
$self->{'_description'} = $arg;
return $arg;
}
if( exists $self->{'_description'} ) {
return $self->{'_description'};
}
......@@ -449,16 +483,19 @@ sub get_all_DBLinks {
=head2 add_DBLink
Title : add_DBLink
Usage :
Function:
Example :
Returns :
Args :
Arg [1] : Bio::Annotation::DBLink $link
a link is a database entry somewhere else.
Usually this is a Bio::EnsEMBL::DBEntry.
Example : none
Description: will add the link to the list of links already in the
gene object.
Returntype : none
Exceptions : none
Caller : general
=cut
sub add_DBLink{
my ($self,$value) = @_;
......@@ -477,20 +514,18 @@ sub add_DBLink{
=head2 get_all_Exons
Title : get_all_Exons
Usage : foreach my $exon ( $gene->each_unique_Exon )
Function: retrieves a listref of exons associated with this
gene, guaranteed to be nonredundant
Example : @exons = @{$gene->get_all_Exons()};
Returns : listref of Bio::EnsEMBL::Exon objects
Args : none
Args : none
Example : none
Description: a set off all the exons associated with this gene.
Returntype : listref Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
=cut
sub get_all_Exons {
my ($self,@args) = @_;
my %h;
......@@ -509,17 +544,19 @@ sub get_all_Exons {
}
=head2 type
Title : type
Usage : $obj->type($newval)
Function:
Returns : value of type
Args : newvalue (optional)
=head2 type
Arg [1] : string $type
Example : none
Description: get/set for attribute type
Returntype : string
Exceptions : none
Caller : general
=cut
sub type {
my $obj = shift;
if( @_ ) {
......@@ -530,18 +567,21 @@ sub type {
}
=head2 add_Transcript
Title : add_Transcript
Usage : $gene->add_Transcript($tr)
Function:
Example :
Returns :
Args :
=head2 add_Transcript
Arg 1 : Bio::EnsEMBL::Transcript $transcript
Example : none
Description: adds another Transcript to the set of alternativly
spliced Transcripts off this gene. If it shares exons
with another Transcript, these should be object-identical
Returntype : none
Exceptions : none
Caller : general
=cut
sub add_Transcript{
my ($self,$trans) = @_;
......@@ -558,17 +598,19 @@ sub add_Transcript{
}
=head2 get_all_Transcripts
Title : get_all_Transcripts
Usage : foreach $trans ( @{$gene->get_all_Transcripts})
Function:
Example :
Returns : A listref of Transcript objects
Args :
Args : none
Example : none
Description: return the Transcripts in this gene
Returntype : listref Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
=cut
sub get_all_Transcripts {
my ($self) = @_;
......@@ -579,15 +621,18 @@ sub get_all_Transcripts {
=head2 created
Title : created
Usage : $obj->created()
Function:
Returns : value of created
Args :
Arg [1] : string $created
The time the stable id for this gene was created. Not very well
maintained data (at release 9)
Example : none
Description: get/set/lazy_load for the created timestamp
Returntype : string
Exceptions : none
Caller : general
=cut
sub created{
my ($self,$value) = @_;
......@@ -606,17 +651,21 @@ sub created{
}
=head2 modified
Title : modified
Usage : $obj->modified()
Function:
Returns : value of modified
Args :
=head2 modified
Arg [1] : string $modified
The time the gene with this stable_id was last modified.
Not well maintained data (release 9)
Example : none
Description: get/set/lazy_load of modified timestamp
Returntype : string
Exceptions : none
Caller : general
=cut
sub modified{
my ($self,$value) = @_;
......@@ -635,16 +684,20 @@ sub modified{
}
=head2 version
Title : version
Usage : $obj->version()
Function:
Returns : value of version
Args :
Arg [1] : int $version
A version number for the stable_id
Example : nonen
Description: get/set/lazy_load for the version number
Returntype : int
Exceptions : none
Caller : general
=cut
sub version{
my ($self,$value) = @_;
......@@ -665,14 +718,15 @@ sub version{
}
=head2 stable_id
Title : stable_id
Usage : $obj->stable_id
Function:
Returns : value of stable_id
Args :
=head2 stable_id
Arg [1] : string $stable_id
Example : ("ENSG0000000001")
Description: get/set/lazy_loaded stable id for this gene
Returntype : string
Exceptions : none
Caller : general
=cut
......@@ -696,6 +750,20 @@ sub stable_id{
}
=head2 _get_stable_entry_info
Args : none
Example : none
Description: does the lazy loading for all stable id related information
Returntype : none
Exceptions : none
Caller : internal
=cut
sub _get_stable_entry_info {
my $self = shift;
......@@ -709,18 +777,6 @@ sub _get_stable_entry_info {
=head2 _dump
Title : _dump
Usage : dump data structure for debugging
Function:
Example :
Returns :
Args :
=cut
sub _dump{
my ($self,$fh) = @_;
......
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