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ensembl-gh-mirror
ensembl
Commits
9d4245db
Commit
9d4245db
authored
Aug 24, 2004
by
Ian Longden
Browse files
add_tracks changes mostly
parent
ee37fb57
Changes
1
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1 changed file
with
18 additions
and
33 deletions
+18
-33
modules/Bio/EnsEMBL/Registry.pm
modules/Bio/EnsEMBL/Registry.pm
+18
-33
No files found.
modules/Bio/EnsEMBL/Registry.pm
View file @
9d4245db
...
...
@@ -150,9 +150,13 @@ sub load_all{
elsif
(
-
e
$ENV
{
HOME
}
.
"
/.ensembl_init
"){
do
(
$ENV
{
HOME
}
.
"
/.ensembl_init
");
}
print
STDERR
"
NO default configuration to load
\n
";
else
{
print
STDERR
"
NO default configuration to load
\n
";
}
}
else
{
print
STDERR
"
Already configured???
\n
";
}
print
STDERR
"
Already configured???
\n
";
}
#=head2 check_if_already_there
...
...
@@ -692,46 +696,27 @@ sub default_track{
=cut
sub
add_new_tracks
{
my
(
$class
,
$conf
)
=
@_
;
my
(
$class
,
$conf
,
$pos
)
=
@_
;
my
$start
=
0
;
my
$reg
=
$class
;
my
$species_reg
=
$reg
->
get_alias
(
$conf
->
{'
species
'},"
nothrow
");
my
$view
=
$conf
->
{'
type
'};
my
%pars
;
print
STDERR
"
Species
$species_reg
check for default tracks
\n
";
if
(
defined
(
$species_reg
)){
my
$config
=
$conf
->
{'
general
'}
->
{
$view
};
foreach
my
$dba
(
$reg
->
get_all_DBAdaptors
()){
# if($dba->species eq $species_reg and !$reg->default_track($dba->species,$dba->group)){
if
(
!
$reg
->
default_track
(
$dba
->
species
,
$dba
->
group
)){
if
(
$start
==
0
){
if
(
exists
(
$config
->
{'
vega_transcript_lite
'})
and
defined
(
$config
->
{'
vega_transcript_lite
'}
->
{'
pos
'})){
$start
=
$config
->
{'
vega_transcript_lite
'}
->
{'
pos
'};
}
elsif
(
exists
(
$config
->
{'
transcript_lite
'})
and
defined
(
$config
->
{'
transcript_lite
'}
->
{'
pos
'})){
$start
=
$config
->
{'
transcript_lite
'}
->
{'
pos
'};
}
else
{
# no transcripts on this view so do not add track here
# print STDERR "no transcript options on this display \n";
next
;
}
$start
++
;
}
else
{
if
(
exists
(
$config
->
{'
vega_transcript_lite
'})
and
defined
(
$config
->
{'
vega_transcript_lite
'}
->
{'
pos
'})){
$start
++
;
}
elsif
(
exists
(
$config
->
{'
transcript_lite
'})
and
defined
(
$config
->
{'
transcript_lite
'}
->
{'
pos
'})){
$start
++
;
}
else
{
# no transcripts on this view so do not add track here
# print STDERR "no transcript options on this display \n";
next
;
}
}
$reg
->
_add_new_track
(
$conf
->
{'
general
'}
->
{
$view
},
$dba
,
$start
);
$pars
{'
available
'}
=
"
species
"
.
$reg
->
get_alias
(
$dba
->
species
());
$pars
{'
db_alias
'}
=
$dba
->
group
();
# print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n";
$conf
->
add_new_track_generictranscript
('',
$dba
->
group
()
.
"
_yo
","
black
",
$pos
,
%pars
);
# my( $self, $code, $text_label, $colour, $pos, %pars ) = @_;
$pos
++
;
}
}
}
return
$pos
;
}
...
...
@@ -747,7 +732,7 @@ sub add_new_tracks{
=cut
sub
_add_new_track
{
my
(
$class
,
$config
,
$dba
,
$start
)
=
@_
;
my
(
$class
,
$conf
,
$config
,
$dba
,
$start
)
=
@_
;
my
$KEY
=
$dba
->
group
();
...
...
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