From f4036606f8428a96319da736392cee7bdfe27826 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 11 Feb 2004 21:23:00 +0000
Subject: [PATCH] modifications so that toplevel is now a pseudo coordinate
system representing the highest real coordinate system in a given region
---
modules/Bio/EnsEMBL/AssemblyMapper.pm | 8 +-
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm | 6 +-
modules/Bio/EnsEMBL/Chromosome.pm | 5 +-
modules/Bio/EnsEMBL/CoordSystem.pm | 95 +++++-
.../EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm | 8 +
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 204 ++++++------
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm | 7 +-
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 7 +-
modules/Bio/EnsEMBL/Feature.pm | 9 +-
modules/Bio/EnsEMBL/Mapper.pm | 66 ++--
modules/Bio/EnsEMBL/Mapper/Coordinate.pm | 53 ++-
modules/Bio/EnsEMBL/Slice.pm | 31 +-
modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm | 308 ++++++++++++++++++
13 files changed, 626 insertions(+), 181 deletions(-)
create mode 100644 modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
diff --git a/modules/Bio/EnsEMBL/AssemblyMapper.pm b/modules/Bio/EnsEMBL/AssemblyMapper.pm
index 683dcd3a31..cbaf833b28 100644
--- a/modules/Bio/EnsEMBL/AssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/AssemblyMapper.pm
@@ -102,7 +102,9 @@ sub new {
#we load the mapper calling the 'ASSEMBLED' the 'from' coord system
#and the 'COMPONENT' the 'to' coord system
- $self->{'mapper'} = Bio::EnsEMBL::Mapper->new($ASSEMBLED, $COMPONENT);
+ $self->{'mapper'} = Bio::EnsEMBL::Mapper->new($ASSEMBLED, $COMPONENT,
+ $coord_systems[0],
+ $coord_systems[1]);
return $self;
}
@@ -186,8 +188,6 @@ sub map {
=cut
-
-
sub flush {
my $self = shift;
@@ -258,7 +258,7 @@ sub fastmap {
Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs
The coordinate system to obtain overlapping ids of
Example : foreach $id ($asm_mapper->list_ids('X',1,1000,$ctg_cs)) {...}
- Description: Retrieves a list of overlapping seq_region internal identifiers
+ Description: Retrieves a list of overlapping seq_region names
of another coordinate system. This is the same as the
list_ids method but uses seq_region names rather internal ids
Returntype : List of strings
diff --git a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
index cdfd072fa8..1cfd7d439a 100644
--- a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
@@ -119,7 +119,9 @@ sub new {
#mapper that is actually used and is loaded by the mappings generated
#by the other two mappers
- $self->{'first_last_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $LAST);
+ $self->{'first_last_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $LAST,
+ $coord_systems[0],
+ $coord_systems[2]);
#need registries to keep track of what regions are registered in source
#and destination coordinate systems
@@ -246,7 +248,7 @@ sub map {
sub fastmap {
my $self = shift;
- $self->map(@_,1);
+ return $self->map(@_,1);
}
diff --git a/modules/Bio/EnsEMBL/Chromosome.pm b/modules/Bio/EnsEMBL/Chromosome.pm
index 2f7649d1ac..8bd68df438 100755
--- a/modules/Bio/EnsEMBL/Chromosome.pm
+++ b/modules/Bio/EnsEMBL/Chromosome.pm
@@ -53,7 +53,10 @@ sub new {
if($chr_name) {
if($adaptor) {
- my $chr = $adaptor->fetch_by_region('toplevel',$chr_name);
+ my $csa = $adaptor->db->get_CoordSystemAdaptor();
+ my ($top_cs) = @{$csa->fetch_all()};
+ my $chr = $adaptor->fetch_by_region($top_cs->name(),$chr_name,
+ undef,undef,undef,$top_cs->version());
bless $chr, 'Bio::EnsEMBL::Chromosome';
return $chr;
} else {
diff --git a/modules/Bio/EnsEMBL/CoordSystem.pm b/modules/Bio/EnsEMBL/CoordSystem.pm
index 73dfa98d76..03d8146d6e 100644
--- a/modules/Bio/EnsEMBL/CoordSystem.pm
+++ b/modules/Bio/EnsEMBL/CoordSystem.pm
@@ -55,7 +55,8 @@ package Bio::EnsEMBL::CoordSystem;
use Bio::EnsEMBL::Storable;
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
use vars qw(@ISA);
@@ -67,24 +68,32 @@ use vars qw(@ISA);
Arg [..] : List of named arguments:
-NAME - The name of the coordinate system
-VERSION - (optional) The version of the coordinate system
+ -RANK - The rank of the coordinate system. The highest
+ level coordinate system should have rank 1, the
+ second highest rank 2 and so on. An example of
+ a high level coordinate system is 'chromosome' an
+ example of a lower level coordinate system is
+ 'clone'.
-TOP_LEVEL - (optional) Sets whether this is a top-level coord
- system. Default = 0
+ system. Default = 0. This should only be set to
+ true if you are creating an artificial toplevel
+ coordsystem by the name of 'toplevel'
-SEQUENCE_LEVEL - (optional) Sets whether this is a sequence
level coordinate system. Default = 0
- -DEFAULT - (optional)
+ -DEFAULT - (optional)
Whether this is the default version of the
coordinate systems of this name. Default = 0
-DBID - (optional) The internal identifier of this
coordinate system
-ADAPTOR - (optional) The adaptor which provides database
interaction for this object
- Example : $cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome',
+ Example : $cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome',
-VERSION => 'NCBI33',
+ -RANK => 1,
-DBID => 1,
-ADAPTOR => adaptor,
-DEFAULT => 1,
- -SEQUENCE_LEVEL => 0,
- -TOP_LEVEL => 1);
+ -SEQUENCE_LEVEL => 0);
Description: Creates a new CoordSystem object representing a coordinate
system.
Returntype : Bio::EnsEMBL::CoordSystem
@@ -99,23 +108,57 @@ sub new {
my $self = $class->SUPER::new(@_);
- my ($name,$version, $top_level, $sequence_level, $default) =
+ my ($name,$version, $top_level, $sequence_level, $default, $rank) =
rearrange(['NAME','VERSION','TOP_LEVEL', 'SEQUENCE_LEVEL',
- 'DEFAULT'], @_);
+ 'DEFAULT', 'RANK'], @_);
throw('The NAME argument is required') if(!$name);
$version = '' if(!defined($version));
- $top_level ||= 0;
- $sequence_level ||= 0;
- $default ||= 0;
+ $top_level = ($top_level) ? 1 : 0;
+ $sequence_level = ($sequence_level) ? 1 : 0;
+ $default = ($default) ? 1 : 0;
+ $rank ||= 0;
+
+ if($top_level) {
+ if($rank) {
+ throw('RANK argument must be 0 if TOP_LEVEL is 1');
+ }
+
+ if($name) {
+ if($name ne 'toplevel') {
+ throw('The NAME argument must be "toplevel" if TOP_LEVEL is 1')
+ }
+ } else {
+ $name = 'toplevel';
+ }
+
+ if($sequence_level) {
+ throw("SEQUENCE_LEVEL argument must be 0 if TOP_LEVEL is 1");
+ }
+
+ $default = 0;
+
+ } else {
+ if(!$rank) {
+ throw("RANK argument must be non-zero if not toplevel CoordSystem");
+ }
+ if($name eq 'toplevel') {
+ throw("Cannot name coord system 'toplevel' unless TOP_LEVEL is 1");
+ }
+ }
+
+ if($rank !~ /^\d+$/) {
+ throw('The RANK argument must be a positive integer');
+ }
$self->{'version'} = $version;
$self->{'name'} = $name;
$self->{'top_level'} = $top_level;
$self->{'sequence_level'} = $sequence_level;
$self->{'default'} = $default;
+ $self->{'rank'} = $rank;
return $self;
}
@@ -196,7 +239,11 @@ sub equals {
Arg [1] : none
Example : if($coord_sys->is_top_level()) { ... }
- Description: Returns true if this is a top level coordinate system
+ Description: Returns true if this is the toplevel pseudo coordinate system.
+ The toplevel coordinate system is not a real coordinate system
+ which is stored in the database, but it is a placeholder that
+ can be used to request transformations or retrievals to/from
+ the highest defined coordinate system in a given region.
Returntype : 0 or 1
Exceptions : none
Caller : general
@@ -244,4 +291,28 @@ sub is_default {
}
+
+
+=head2 rank
+
+ Arg [1] : none
+ Example : if($cs1->rank() < $cs2->rank()) {
+ print $cs1->name(), " is a higher level coord system than",
+ $cs2->name(), "\n";
+ }
+ Description: Returns the rank of this coordinate system. A lower number
+ is a higher coordinate system. The highest level coordinate
+ system has a rank of 1 (e.g. 'chromosome'). The toplevel
+ pseudo coordinate system has a rank of 0.
+ Returntype : int
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub rank {
+ my $self = shift;
+ return $self->{'rank'};
+}
+
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index f3fb19925c..bf09e81ec7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -65,6 +65,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::AssemblyMapper;
use Bio::EnsEMBL::ChainedAssemblyMapper;
+use Bio::EnsEMBL::TopLevelAssemblyMapper;
use Bio::EnsEMBL::Utils::Cache; #CPAN LRU cache
use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
@@ -146,6 +147,13 @@ sub fetch_by_CoordSystems {
$cs1->name . " " . $cs1->version);
}
+ if($cs1->is_top_level()) {
+ return Bio::EnsEMBL::TopLevelAssemblyMapper->new($self, $cs1, $cs2);
+ }
+ if($cs2->is_top_level()) {
+ return Bio::EnsEMBL::TopLevelAssemblyMapper->new($self, $cs2, $cs1);
+ }
+
my $csa = $self->db->get_CoordSystemAdaptor();
#retrieve the shortest possible mapping path between these systems
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index 2542b6cef7..a9518dc1bd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -36,23 +36,23 @@ Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
}
#
- # Fetching by top level:
+ # Fetching by rank:
+ #
+ $cs = $csa->fetch_by_rank(2);
+
+ #
+ # Fetching the pseudo coord system 'toplevel'
#
#Get the default top_level coord system:
$cs = $csa->fetch_top_level();
- #Get a particular version of a top_level coord system:
- $cs = $csa->fetch_top_level('NCBI34');
-
- #Get all top level coord systems:
- foreach $cs (@{$csa->fetch_all_top_level()}) {
- print $cs->name(), ' ', $cs->version, "\n";
- }
-
#can also use an alias in fetch_by_name:
$cs = $csa->fetch_by_name('toplevel');
+ #can also request toplevel using rank=0
+ $cs = $csa->fetch_by_rank(0);
+
#
# Fetching by sequence level:
#
@@ -87,10 +87,7 @@ not have a version an empty string ('') is used instead.
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
+=head1 METHODS
=cut
@@ -102,7 +99,6 @@ package Bio::EnsEMBL::DBSQL::CoordSystemAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::CoordSystem;
-use DBI;
use vars qw(@ISA);
@@ -140,30 +136,29 @@ sub new {
#keyed on id, coord_system value
$self->{'_dbID_cache'} = {};
+ #keyed on rank
+ $self->{'_rank_cache'} = {};
+
#keyed on id, 1/undef values
$self->{'_is_sequence_level'} = {};
- $self->{'_is_top_level'} = {};
$self->{'_is_default_version'} = {};
- my $sth = $self->prepare('SELECT coord_system_id, name, version, attrib ' .
- 'FROM coord_system');
-
+ my $sth = $self->prepare(
+ 'SELECT coord_system_id, name, rank, version, attrib ' .
+ 'FROM coord_system');
$sth->execute();
- my ($dbID, $name, $version, $attrib);
- $sth->bind_columns(\$dbID, \$name, \$version, \$attrib);
+ my ($dbID, $name, $rank, $version, $attrib);
+ $sth->bind_columns(\$dbID, \$name, \$rank, \$version, \$attrib);
while($sth->fetch()) {
my $seq_lvl = 0;
- my $top_lvl = 0;
my $default = 0;
if($attrib) {
foreach my $attrib (split(',', $attrib)) {
$self->{"_is_$attrib"}->{$dbID} = 1;
if($attrib eq 'sequence_level') {
$seq_lvl = 1;
- } elsif($attrib eq 'top_level') {
- $top_lvl = 1;
} elsif($attrib eq 'default_version') {
$default = 1;
}
@@ -175,13 +170,14 @@ sub new {
-ADAPTOR => $self,
-NAME => $name,
-VERSION => $version,
- -TOP_LEVEL => $top_lvl,
+ -RANK => $rank,
-SEQUENCE_LEVEL => $seq_lvl,
-DEFAULT => $default);
$self->{'_dbID_cache'}->{$dbID} = $cs;
$self->{'_name_cache'}->{lc($name)} ||= [];
+ $self->{'_rank_cache'}->{$rank} = $cs;
push @{$self->{'_name_cache'}->{lc($name)}}, $cs;
}
$sth->finish();
@@ -225,6 +221,15 @@ sub new {
$mappings{$asm_cs->dbID}->{$cmp_cs->dbID} = 1;
}
+ #
+ # Create the pseudo coord system 'toplevel' and cache it so that
+ # only one of these is created for each db...
+ #
+ my $toplevel = Bio::EnsEMBL::CoordSystem->new(-TOP_LEVEL => 1,
+ -NAME => 'toplevel',
+ -ADAPTOR => $self);
+ $self->{'_top_level'} = $toplevel;
+
$self->{'_mapping_paths'} = \%mappings;
return $self;
@@ -238,7 +243,10 @@ sub new {
Example : foreach my $cs (@{$csa->fetch_all()}) {
print $cs->name(), ' ', $cs->version(), "\n";
}
- Description: Retrieves every coordinate system defined in the DB
+ Description: Retrieves every coordinate system defined in the DB.
+ These will be returned in ascending order of rank. I.e.
+ The highest coordinate system with rank=1 would be first in the
+ array.
Returntype : listref of Bio::EnsEMBL::CoordSystems
Exceptions : none
Caller : general
@@ -248,13 +256,47 @@ sub new {
sub fetch_all {
my $self = shift;
- my @coord_systems = values %{$self->{'_dbID_cache'}};
+ my @coord_systems;
+
+ #order the array by rank in ascending order
+ foreach my $rank (sort {$a <=> $b} keys %{$self->{'_rank_cache'}}) {
+ push @coord_systems, $self->{'_rank_cache'}->{$rank};
+ }
return \@coord_systems;
}
+=head2 fetch_by_rank
+
+ Arg [1] : int $rank
+ Example : my $cs = $coord_sys_adaptor->fetch_by_rank(1);
+ Description: Retrieves a CoordinateSystem via its rank. 0 is a special
+ rank reserved for the pseudo coordinate system 'toplevel'.
+ undef is returned if no coordinate system of the specified rank
+ exists.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub fetch_by_rank {
+ my $self = shift;
+ my $rank = shift;
+
+ throw("Rank argument must be defined.") if(!defined($rank));
+ throw("Rank argument must be a non-negative integer.") if($rank !~ /^\d+$/);
+
+ if($rank == 0) {
+ return $self->fetch_top_level();
+ }
+
+ return $self->{'_rank_cache'}->{$rank};
+}
+
+
=head2 fetch_by_name
Arg [1] : string $name
@@ -266,17 +308,16 @@ sub fetch_all {
specified the default version will be used.
Example : $coord_sys = $csa->fetch_by_name('clone');
$coord_sys = $csa->fetch_by_name('chromosome', 'NCBI33');
- #toplevel is an alias for the highest coordinate system
- #such as the chromosome coordinate system
+ # toplevel is an pseudo coord system representing the highest
+ # coord system in a given region
+ # such as the chromosome coordinate system
$coord_sys = $csa->fetch_by_name('toplevel');
- $coord_sys = $csa->fetch_by_name('toplevel', 'NCBI31');
#seqlevel is an alias for the sequence level coordinate system
#such as the clone or contig coordinate system
$coord_sys = $csa->fetch_by_name('seqlevel');
Description: Retrieves a coordinate system by its name
Returntype : Bio::EnsEMBL::CoordSystem
- Exceptions : throw if the requested coordinate system does not exist
- throw if no name argument provided
+ Exceptions : throw if no name argument provided
warning if no version provided and default does not exist
Caller : general
@@ -299,19 +340,16 @@ sub fetch_by_name {
}
if(!exists($self->{'_name_cache'}->{$name})) {
- my $guess = '';
if($name =~ /top/) {
- $guess = "\nDid you mean 'toplevel' instead of '$name'?";
+ warning("Did you mean 'toplevel' coord system instead of '$name'?");
} elsif($name =~ /seq/) {
- $guess = "\nDid you mean 'seqlevel' instead of '$name'?";
+ warning("Did you mean 'seqlevel' coord system instead of '$name'?");
}
- throw("Coord_system with name [$name] does not exist.$guess");
+ return undef;
}
my @coord_systems = @{$self->{'_name_cache'}->{$name}};
- throw("Coord_system with name [$name] does not exist.") if(!@coord_systems);
-
foreach my $cs (@coord_systems) {
if($version) {
return $cs if(lc($cs->version()) eq $version);
@@ -321,7 +359,8 @@ sub fetch_by_name {
}
if($version) {
- throw("Coord_system [$name] does not exist with version [$version]");
+ #the specific version we were looking for was not found
+ return undef;
}
#didn't find a default, just take first one
@@ -359,7 +398,7 @@ sub fetch_all_by_name {
if($name eq 'seqlevel') {
return [$self->fetch_sequence_level()];
} elsif($name eq 'toplevel') {
- return $self->fetch_all_top_level();
+ return [$self->fetch_top_level()];
}
return $self->{'_name_cache'}->{$name} || [];
@@ -469,8 +508,9 @@ sub add_feature_table {
Arg [1] : int dbID
Example : $cs = $csa->fetch_by_dbID(4);
Description: Retrieves a coord_system via its internal
- identifier.
- Returntype : Bio::EnsEMBL::CoordSystem
+ identifier, or undef if no coordinate system with the provided
+ id exists.
+ Returntype : Bio::EnsEMBL::CoordSystem or undef
Exceptions : thrown if no coord_system exists for specified dbID
Caller : general
@@ -484,7 +524,7 @@ sub fetch_by_dbID {
my $cs = $self->{'_dbID_cache'}->{$dbID};
- throw("Coord_system with dbID [$dbID] does not exist") if(!$cs);
+ return undef if(!$cs);
return $cs;
}
@@ -493,63 +533,22 @@ sub fetch_by_dbID {
=head2 fetch_top_level
- Arg [1] : string $version (optional)
- The version of the top-level to obtain. If not provided
- the default version top-level will be returned.
+ Arg [1] : none
Example : $cs = $csa->fetch_top_level();
- $cs = $csa->fetch_top_level('NCBI34');
- Description: Retrieves the top level coordinate system. It is possible
- to have multiple top-level coordinate systems if there is
- more than one version of the top-level system. For
- example the top level of a homo_sapiens database could
- be 'chromosome' but this might have 'NCBI33', 'NCBI31',
- and 'NCBI34' versions. One of these will be defined as
- the default and will be returned if no specific version
- is requested. If a specific version is requested then it
- will be returned.
+ Description: Retrieves the toplevel pseudo coordinate system.
Returntype : a Bio::EnsEMBL::CoordSystem object
- Exceptions : throw if no top-level coord_system exists for specified
- version
- throw if no top-level coord_system exists at all
- warning if no version specified and no default version
- exists
- Caller : general
-
-=cut
-
-sub fetch_top_level {
- my $self = shift;
-
- return $self->_fetch_by_attrib('top_level', @_);
-}
-
-
-=head2 fetch_all_top_level
-
- Arg [1] : none
- Example : foreach my $cs (@{$csa->fetch_all_top_level()}) {
- my ($id, $name, $version) = @$cs;
- }
- Description: Retrieves all top level coordinate systems defined in
- the DB. It is possible to have multiple top-level
- coordinate systems if there is more than one version
- of the top-level system. For example the top level of a
- homo_sapiens database could be 'chromosome' but this
- might have 'NCBI33', 'NCBI31', and 'NCBI34' versions.
- Returntype : listref of Bio::EnsEMBL::CoordSystem objects
Exceptions : none
Caller : general
=cut
-sub fetch_all_top_level {
+sub fetch_top_level {
my $self = shift;
- return $self->_fetch_all_by_attrib('top_level', @_);
+ return $self->{'_top_level'};
}
-
=head2 fetch_sequence_level
Arg [1] : none
@@ -797,6 +796,7 @@ sub deleteObj {
delete $self->{'_dbID_cache'};
delete $self->{'_mapping_paths'};
delete $self->{'_shortest_paths'};
+ delete $self->{'_top_level'};
}
@@ -822,10 +822,17 @@ sub store {
my $db = $self->db();
my $name = $cs->name();
my $version = $cs->version();
- my $toplevel = $cs->is_top_level();
+ my $rank = $cs->rank();
+
my $seqlevel = $cs->is_sequence_level();
my $default = $cs->is_default();
-
+
+ my $toplevel = $cs->is_top_level();
+
+ if($toplevel) {
+ throw("The toplevel CoordSystem cannot be stored");
+ }
+
#
# Do lots of sanity checking to prevent bad data from being entered
#
@@ -856,9 +863,19 @@ sub store {
}
}
+ if($rank !~ /^\d+$/) {
+ throw("Rank attribute must be a positive integer not [$rank]");
+ }
+ if($rank == 0) {
+ throw("Only toplevel CoordSystem may have rank of 0.");
+ }
+
+ if(defined($self->{'_rank_cache'}->{$rank})) {
+ throw("CoordSystem with rank [$rank] already exists.");
+ }
+
my @attrib;
- push @attrib, 'top_level' if($toplevel);
push @attrib, 'default_version' if($default);
push @attrib, 'sequence_level' if($seqlevel);
@@ -871,9 +888,10 @@ sub store {
my $sth = $db->prepare('INSERT INTO coord_system ' .
'SET name = ?, ' .
'version = ?, ' .
- 'attrib = ?');
+ 'attrib = ?,' .
+ 'rank = ?');
- $sth->execute($name, $version, $attrib_str);
+ $sth->execute($name, $version, $attrib_str, $rank);
my $dbID = $sth->{'mysql_insertid'};
$sth->finish();
@@ -889,12 +907,12 @@ sub store {
#
$self->{'_is_default_version'}->{$dbID} = 1 if($default);
$self->{'_is_sequence_level'}->{$dbID} = 1 if($seqlevel);
- $self->{'_is_top_level'}->{$dbID} = 1 if($toplevel);
$self->{'_name_cache'}->{lc($name)} ||= [];
push @{$self->{'_name_cache'}->{lc($name)}}, $cs;
$self->{'_dbID_cache'}->{$dbID} = $cs;
+ $self->{'_rank_cache'}->{$rank} = $cs;
return $cs;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index 6af66ae180..94fd5ef64b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -267,10 +267,13 @@ sub fetch_by_assembly_location {
deprecate('Use fetch_by_Slice_start_end_strand() instead');
+ my $csa = $self->db->get_CoordSystem();
+ my $top_cs = @{$csa->fetch_all};
+
my $slice_adaptor = $self->db->get_SliceAdaptor();
- my $slice = $slice_adaptor->fetch_by_region('toplevel', $chrName,
+ my $slice = $slice_adaptor->fetch_by_region($top_cs->name(), $chrName,
$chrStart, $chrEnd,
- $strand);
+ $strand, $top_cs->version);
return $self->fetch_by_Slice_start_end_strand($slice,1, $slice->length,1);
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index e6aca82fc3..9ef007b681 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -1446,7 +1446,12 @@ sub fetch_by_chr_name{
my ($self,$chr_name) = @_;
deprecate('Use fetch_by_region() instead.');
- return $self->fetch_by_region('toplevel',$chr_name);
+ my $csa = $self->db->get_CoordSystemAdaptor();
+
+ my $top_cs = @{$csa->fetch_all()};
+
+ return $self->fetch_by_region($top_cs->name(),$chr_name,
+ undef,undef,undef,$top_cs->version);
}
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index eb1b7618d0..82ba9552b0 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -392,8 +392,10 @@ sub transform {
my $cs = $db->get_CoordSystemAdaptor->fetch_by_name($cs_name, $cs_version);
my $current_cs = $slice->coord_system();
- # self is already in the requested coordinate system, so we can just return a copy
- if( $cs->equals( $current_cs ) && $slice->start() == 1 && $slice->strand() == 1 ) {
+ # if feature is already in the requested coordinate system, we can just
+ # return a copy
+ if( $cs->equals( $current_cs ) && $slice->start() == 1 &&
+ $slice->strand() == 1 ) {
my $new_feature;
%$new_feature = %$self;
bless $new_feature, ref $self;
@@ -418,7 +420,8 @@ sub transform {
bless $new_feature, ref $self;
$new_feature->{'start'} = $p_slice->start();
$new_feature->{'end'} = $p_slice->end();
- $new_feature->{'strand'} = ($self->{'strand'} == 0) ? 0 : $p_slice->strand();
+ $new_feature->{'strand'} =
+ ($self->{'strand'} == 0) ? 0 : $p_slice->strand();
$new_feature->{'slice'} = $slice;
return $new_feature;
}
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index cea829dba5..d599e52e66 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -56,11 +56,30 @@ use Bio::EnsEMBL::Mapper::Gap;
use Bio::EnsEMBL::Utils::Exception qw(throw);
-sub new {
- my($class,@args) = @_;
- my $from = shift @args;
- my $to = shift @args;
+=head2 new
+
+ Arg [1] : string $from
+ The name of the 'from' coordinate system
+ Arg [2] : string $to
+ The name of the 'to' coordinate system
+ Arg [3] : (optional) Bio::EnsEMBL::CoordSystem $from_cs
+ The 'from' coordinate system
+ Arg [4] : (optional) Bio::EnsEMBL::CoordSystem $to_cs
+ Example : my $mapper = Bio::EnsEMBL::Mapper->new('FROM', 'TO');
+ Description: Constructor. Creates a new Bio::EnsEMBL::Mapper object.
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub new {
+ my $class = shift;
+ my $from = shift;
+ my $to = shift;
+ my $from_cs = shift;
+ my $to_cs = shift;
my $self = {};
bless $self,$class;
@@ -76,7 +95,10 @@ sub new {
$self->from($from);
$self->{'pair_count'} = 0;
-# set stuff in self from @args
+
+ $self->{'from_cs'} = $from_cs;
+ $self->{'to_cs'} = $to_cs;
+
return $self;
}
@@ -130,8 +152,6 @@ sub flush {
sub map_coordinates{
my ($self, $id, $start, $end, $strand, $type) = @_;
- #&eprof_start('map_coordinates');
-
unless(defined($id) && defined($start) && defined($end) &&
defined($strand) && defined($type) ) {
throw("Must start,end,strand,id,type as coordinates");
@@ -142,14 +162,16 @@ sub map_coordinates{
my $hash = $self->{"_pair_$type"};
- my ($from, $to);
+ my ($from, $to, $cs);
if($type eq $self->{'to'}) {
$from = 'to';
$to = 'from';
+ $cs = $self->{'from_cs'};
} else {
$from = 'from';
$to = 'to';
+ $cs = $self->{'to_cs'};
}
unless(defined $hash) {
@@ -244,7 +266,8 @@ sub map_coordinates{
my $res = Bio::EnsEMBL::Mapper::Coordinate->new($target_coord->{'id'},
$target_start,
$target_end,
- $pair->{'ori'} * $strand);
+ $pair->{'ori'} * $strand,
+ $cs);
push(@result,$res);
$last_used_pair = $pair;
@@ -267,8 +290,6 @@ sub map_coordinates{
@result = reverse ( @result);
}
- #&eprof_end('map_coordinates');
-
return @result;
}
@@ -296,16 +317,18 @@ sub map_coordinates{
sub fastmap {
my ($self, $id, $start, $end, $strand, $type) = @_;
- my ($from, $to);
+ my ($from, $to, $cs);
if( ! $self->{'_is_sorted'} ) { $self->_sort() }
if($type eq $self->{'to'}) {
$from = 'to';
$to = 'from';
+ $cs = $self->{'from_cs'};
} else {
$from = 'from';
$to = 'to';
+ $cs = $self->{'to_cs'};
}
my $hash = $self->{"_pair_$type"} or
@@ -317,25 +340,24 @@ sub fastmap {
foreach my $pair (@$pairs) {
my $self_coord = $pair->{$from};
my $target_coord = $pair->{$to};
-
+
# only super easy mapping is done
if( $start < $self_coord->{'start'} ||
- $end > $self_coord->{'end'} ) {
+ $end > $self_coord->{'end'} ) {
next;
}
-
+
if( $pair->{'ori'} == 1 ) {
return ( $target_coord->{'id'},
- $target_coord->{'start'}+$start-$self_coord->{'start'},
- $target_coord->{'start'}+$end-$self_coord->{'start'},
- $strand );
+ $target_coord->{'start'}+$start-$self_coord->{'start'},
+ $target_coord->{'start'}+$end-$self_coord->{'start'},
+ $strand, $cs );
} else {
return ( $target_coord->{'id'},
- $target_coord->{'end'} - ($end - $self_coord->{'start'}),
- $target_coord->{'end'} - ($start - $self_coord->{'start'}),
- -$strand );
+ $target_coord->{'end'} - ($end - $self_coord->{'start'}),
+ $target_coord->{'end'} - ($start - $self_coord->{'start'}),
+ -$strand, $cs );
}
-
}
return ();
diff --git a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
index 8cbeb0ab13..818424a29d 100644
--- a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
@@ -36,12 +36,13 @@ use vars qw(@ISA);
use strict;
sub new {
- my($class, $id, $start, $end, $strand) = @_;
+ my($class, $id, $start, $end, $strand, $coord_system) = @_;
return bless { 'id' => $id,
- 'start' => $start,
- 'end' => $end,
- 'strand' => $strand }, $class;
+ 'start' => $start,
+ 'end' => $end,
+ 'strand' => $strand,
+ 'coord_system' => $coord_system}, $class;
}
@@ -57,13 +58,9 @@ sub new {
=cut
sub start{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'start'} = $value;
- }
- return $obj->{'start'};
-
+ my $self = shift;
+ $self->{'start'} = shift if(@_);
+ return $self->{'start'};
}
@@ -79,13 +76,9 @@ sub start{
=cut
sub end{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'end'} = $value;
- }
- return $obj->{'end'};
-
+ my $self = shift;
+ $self->{'end'} = shift if(@_);
+ return $self->{'end'};
}
@@ -101,13 +94,9 @@ sub end{
=cut
sub strand{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'strand'} = $value;
- }
- return $obj->{'strand'};
-
+ my $self = shift;
+ $self->{'strand'} = shift if(@_);
+ return $self->{'strand'};
}
@@ -124,12 +113,16 @@ sub strand{
=cut
sub id{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'id'} = $value;
- }
- return $self->{'id'};
+ my $self = shift;
+ $self->{'id'} = shift if(@_);
+ return $self->{'id'};
+}
+
+sub coord_system {
+ my $self = shift;
+ $self->{'coord_system'} = shift if(@_);
+ return $self->{'coord_system'};
}
sub length {
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index e0c92050f9..b7ad77f9e1 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -148,7 +148,9 @@ sub new {
}
if(!$coord_system || !ref($coord_system) ||
!$coord_system->isa('Bio::EnsEMBL::CoordSystem')) {
- throw('COORD_SYSTEM argment must be a Bio::EnsEMBL::CoordSystem');
+ throw('COORD_SYSTEM argument must be a Bio::EnsEMBL::CoordSystem');
+ } elsif($coord_system->is_top_level()) {
+ throw('Cannot create slice on toplevel CoordSystem.');
}
#strand defaults to 1 if not defined
@@ -615,7 +617,7 @@ sub project {
#if the slice has negative coordinates or coordinates exceeding the
#exceeding length of the sequence region we want to shrink the slice to
#the defined region
-
+
if($self->{'start'} > $entire_len || $self->{'end'} < 1) {
#none of this slice is in a defined region
return [];
@@ -642,8 +644,8 @@ sub project {
my @projection;
my $current_start = 1;
-
- #decompose this slice into its symlinked components.
+
+ #decompose this slice into its symlinked components.
#this allows us to handle haplotypes and PARs
my $normal_slice_proj =
$slice_adaptor->fetch_normalized_slice_projection($self);
@@ -651,12 +653,12 @@ sub project {
my $normal_slice = $segment->[2];
$slice_cs = $normal_slice->coord_system();
-
+
my $asma = $db->get_AssemblyMapperAdaptor();
my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs);
# perform the mapping between this slice and the requested system
- my @coords = $asm_mapper->map($normal_slice->seq_region_name(),
+ my @coords = $asm_mapper->map($normal_slice->seq_region_name(),
$normal_slice->start(),
$normal_slice->end(),
$normal_slice->strand(),
@@ -667,17 +669,19 @@ sub project {
foreach my $coord (@coords) {
my $coord_start = $coord->start();
my $coord_end = $coord->end();
- my $length = $coord_end - $coord_start + 1;
+ my $length = $coord_end - $coord_start + 1;
#skip gaps
if($coord->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+ my $coord_cs = $coord->coord_system();
+
#create slices for the mapped-to coord system
- my $slice = $slice_adaptor->fetch_by_region($cs->name(),
+ my $slice = $slice_adaptor->fetch_by_region($coord_cs->name(),
$coord->id(),
$coord_start,
$coord_end,
$coord->strand(),
- $cs->version());
+ $coord_cs->version());
my $current_end = $current_start + $length - 1;
@@ -1775,8 +1779,13 @@ sub get_Chromosome {
deprecate("Use SliceAdaptor::fetch_by_region('chromosome'," .
'$slice->seq_region_name) instead');
- my $chr = $self->adaptor->fetch_by_region('toplevel',
- $self->seq_region_name());
+ my $csa = $self->adaptor->db->get_CoordSystemAdaptor();
+ my ($top_cs) = @{$csa->fetch_all()};
+
+ my $chr = $self->adaptor->fetch_by_region($top_cs->name(),
+ $self->seq_region_name(),
+ undef,undef,undef,
+ $top_cs->version());
return bless($chr, 'Bio::EnsEMBL::Chromosome');
}
diff --git a/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm b/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
new file mode 100644
index 0000000000..b95b2a9fb2
--- /dev/null
+++ b/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
@@ -0,0 +1,308 @@
+#
+# Ensembl module for Bio::EnsEMBL::AssemblyMapper
+#
+# Written by Graham McVicker
+#
+# Copyright GRL and EBI
+#
+# You may distribute this module under the same terms as perl itself
+
+=head1 NAME
+
+Bio::EnsEMBL::TopLevelMapper -
+Handles mapping between a given coordinate system and the toplevel pseudo
+coordinate system.
+
+=head1 SYNOPSIS
+ $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+ $asma = $db->get_AssemblyMapperAdaptor();
+ $csa = $db->get_CoordSystemAdaptor();
+
+ my $toplevel = $cs_adaptor->fetch_by_name('toplevel');
+ my $ctg_cs = $cs_adaptor->fetch_by_name('contig');
+
+ $asm_mapper = $map_adaptor->fetch_by_CoordSystems($cs1, $cs2);
+
+ #map to toplevel coord system for this region
+ @chr_coords = $asm_mapper->map('AL30421.1.200.92341',100,10000,-1,$ctg_cs);
+
+ #list toplevel seq_region_ids for this region
+ @chr_ids = $asm_mapper->list_ids('AL30421.1.200.92341',1,1000,-1,$ctg_cs);
+
+=head1 DESCRIPTION
+
+The TopLevelAssemblyMapper performs mapping between a provided coordinate
+system and the toplevel pseudo cooordinate system. The toplevel coordinate
+system is not a real coordinate system, but represents the highest coordinate
+system that can be mapped to in a given region. It is only possible to
+perform unidirectional mapping using this mapper, because it does not make
+sense to map from the toplevel coordinate system to another coordinate system.
+
+=head1 CONTACT
+
+Post general queries to B<ensembl-dev@ebi.ac.uk>
+
+=head1 METHODS
+
+=cut
+
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::TopLevelAssemblyMapper;
+
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use Bio::EnsEMBL::Mapper;
+use Bio::EnsEMBL::CoordSystem;
+
+sub new {
+ my ($caller, $adaptor, $toplevel_cs, $other_cs) = @_;
+
+ my $class = ref($caller) || $caller;
+
+ if(!ref($toplevel_cs)) {
+ throw('Toplevel CoordSystem argument expected.');
+ }
+ if(!ref($other_cs)) {
+ throw('Other CoordSystem argument expected.');
+ }
+
+ if(!$toplevel_cs->is_top_level()) {
+ throw($toplevel_cs->name() . " is not the toplevel CoordSystem.");
+ }
+ if($other_cs->is_top_level()) {
+ throw("Other CoordSystem argument should not be toplevel CoordSystem.");
+ }
+
+ my $cs_adaptor = $adaptor->db()->get_CoordSystemAdaptor();
+ my $coord_systems = $cs_adaptor->fetch_all();
+
+ return bless {'coord_systems' => $coord_systems,
+ 'adaptor' => $adaptor,
+ 'toplevel_cs' => $toplevel_cs,
+ 'other_cs' => $other_cs}, $class;
+}
+
+sub adaptor {
+ my $self = shift;
+
+ $self->{'adaptor'} = shift if(@_);
+
+ return $self->{'adaptor'};
+}
+
+
+sub map {
+ throw('Incorrect number of arguments.') if(@_ != 6);
+
+ my($self, $frm_seq_region, $frm_start, $frm_end, $frm_strand, $frm_cs,
+ $fastmap) = @_;
+
+ my $mapper = $self->{'mapper'};
+ my $toplevel_cs = $self->{'toplevel_cs'};
+ my $other_cs = $self->{'other_cs'};
+ my $adaptor = $self->{'adaptor'};
+
+ if($frm_cs->is_top_level()) {
+ throw("The toplevel CoordSystem can only be mapped TO, not FROM.");
+ }
+ if($frm_cs != $other_cs && !$frm_cs->equals($other_cs)) {
+ throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
+ " is neither the assembled nor the component coordinate system " .
+ " of this AssemblyMapper");
+ }
+
+ my $coord_systems = $self->{'coord_systems'};
+
+ my $csa = $self->adaptor()->db()->get_CoordSystemAdaptor();
+
+ #
+ # TBD try to make this more efficient
+ #
+ my $from_rank = $other_cs->rank();
+ foreach my $cs (@$coord_systems) {
+ last if($cs->rank >= $from_rank);
+
+ #check if a mapping path even exists to this coordinate system
+ my @mapping_path = $csa->get_mapping_path($cs,$other_cs);
+
+ if(@mapping_path) {
+
+ # Try to map to this coord system. If we get back any coordinates then
+ # it is our 'toplevel' that we were looking for
+ my $mapper = $adaptor->fetch_by_CoordSystems($other_cs, $cs);
+
+ if($fastmap) {
+ my @result = $mapper->fastmap($frm_seq_region, $frm_start, $frm_end,
+ $frm_strand, $frm_cs);
+ return @result if(@result);
+ } else {
+ my @coords = $mapper->map($frm_seq_region, $frm_start, $frm_end,
+ $frm_strand, $frm_cs);
+
+ if(@coords > 1 || !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap')) {
+ return @coords;
+ }
+ }
+ }
+ }
+
+ # the toplevel coordinate system for the region requested *is* the
+ # requested region.
+ if($fastmap) {
+ return ($frm_seq_region,$frm_start, $frm_end, $frm_strand, $other_cs);
+ }
+ return Bio::EnsEMBL::Mapper::Coordinate->new
+ ($frm_seq_region,$frm_start,$frm_end, $frm_strand, $other_cs);
+}
+
+#
+# for polymorphism with AssemblyMapper
+#
+sub flush {}
+
+sub fastmap {
+ my $self = shift;
+ return $self->map(@_,1);
+}
+
+sub assembled_CoordSystem {
+ my $self = shift;
+ return $self->{'toplevel_cs'};
+}
+
+sub component_CoordSystem {
+ my $self = shift;
+ return $self->{'other_cs'};
+}
+
+
+sub _list {
+ my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs, $seq_regions) = @_;
+
+ my $mapper = $self->{'mapper'};
+ my $toplevel_cs = $self->{'toplevel_cs'};
+ my $other_cs = $self->{'other_cs'};
+ my $adaptor = $self->{'adaptor'};
+
+ if($frm_cs->is_top_level()) {
+ throw("The toplevel CoordSystem can only be mapped TO, not FROM.");
+ }
+ if($frm_cs != $other_cs && !$frm_cs->equals($other_cs)) {
+ throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
+ " is neither the assembled nor the component coordinate system " .
+ " of this AssemblyMapper");
+ }
+
+ my $coord_systems = $self->{'coord_systems'};
+ my $csa = $self->adaptor()->db()->get_CoordSystemAdaptor();
+
+ #
+ # TBD try to make this more efficient
+ #
+ my $from_rank = $other_cs->rank();
+ foreach my $cs (@$coord_systems) {
+ last if($cs->rank >= $from_rank);
+
+ #check if a mapping path even exists to this coordinate system
+ my @mapping_path = $csa->get_mapping_path($cs, $other_cs);
+
+ if(@mapping_path) {
+
+ # Try to map to this coord system. If we get back any coordinates then
+ # it is our 'toplevel' that we were looking for
+ my $mapper = $adaptor->fetch_by_CoordSystems($other_cs, $cs);
+
+ my @result;
+
+ if($seq_regions) {
+ @result = $mapper->list_seq_regions($frm_seq_region, $frm_start,
+ $frm_end, $frm_cs);
+ } else {
+ @result = $mapper->list_ids($frm_seq_region, $frm_start,
+ $frm_end, $frm_cs);
+ }
+
+ return @result if(@result);
+ }
+ }
+
+ # the toplevel coordinate system for the region requested *is* the
+ return ($frm_seq_region);
+
+
+ # requested region.
+ if($seq_regions) {
+ return ($frm_seq_region);
+ }
+
+ #this seems a bit silly and inefficient, but it is probably never
+ #called anyway.
+ my $slice_adaptor = $adaptor->db()->get_SliceAdaptor();
+ my $slice = $slice_adaptor->fetch_by_region($other_cs->name(),
+ $frm_seq_region,
+ undef,undef,undef,$other_cs);
+ return ($slice_adaptor->get_seq_region_id($slice));
+}
+
+
+
+=head2 list_seq_regions
+
+ Arg [1] : string $frm_seq_region
+ The name of the sequence region of interest
+ Arg [2] : int $frm_start
+ The start of the region of interest
+ Arg [3] : int $frm_end
+ The end of the region to transform of interest
+ Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs
+ The coordinate system to obtain overlapping ids of
+ Example : foreach $id ($asm_mapper->list_ids('X',1,1000,$ctg_cs)) {...}
+ Description: Retrieves a list of overlapping seq_region names
+ of another coordinate system. This is the same as the
+ list_ids method but uses seq_region names rather internal ids
+ Returntype : List of strings
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub list_seq_regions {
+ throw('Incorrect number of arguments.') if(@_ != 5);
+ return _list(@_,1);
+}
+
+
+=head2 list_ids
+
+ Arg [1] : string $frm_seq_region
+ The name of the sequence region of interest.
+ Arg [2] : int $frm_start
+ The start of the region of interest
+ Arg [3] : int $frm_end
+ The end of the region to transform of interest
+ Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs
+ The coordinate system to obtain overlapping ids of
+ Example : foreach $id ($asm_mapper->list_ids('X',1,1000,$chr_cs)) {...}
+ Description: Retrieves a list of overlapping seq_region internal identifiers
+ of another coordinate system. This is the same as the
+ list_seq_regions method but uses internal identfiers rather
+ than seq_region strings
+ Returntype : List of ints
+ Exceptions : thrown if the from CoordSystem is the toplevel coord system
+ thrown if the from CoordSystem is not the one used in the mapper
+ Caller : general
+
+=cut
+
+sub list_ids {
+ throw('Incorrect number of arguments.') if(@_ != 5);
+ return _list(@_,0);
+}
+
+
+
+
+
+1;
--
GitLab