diff --git a/modules/Bio/EnsEMBL/EMBLLOAD/Clone.pm b/modules/Bio/EnsEMBL/EMBLLOAD/Clone.pm
index 4cf3d2a6be381ad9a8f5fed1993f4b068f20f521..890e8d68014b118ad86ab10d59ee726120a048a7 100755
--- a/modules/Bio/EnsEMBL/EMBLLOAD/Clone.pm
+++ b/modules/Bio/EnsEMBL/EMBLLOAD/Clone.pm
@@ -49,6 +49,8 @@ use Bio::Root::RootI;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::EMBLLOAD::Contig;
+use Bio::EnsEMBL::DB::CloneI;
+
@ISA = qw(Bio::Root::RootI Bio::EnsEMBL::DB::CloneI);
use Bio::EnsEMBL::Translation;
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
new file mode 100644
index 0000000000000000000000000000000000000000..d845a9d42f89669ff99a88788b947f7e6f2dddf6
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -0,0 +1,410 @@
+
+
+#
+# Ensembl module for Bio::EnsEMBL::Mapper
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+
+ $map->add_map_coordinates( $contig_start, $contig_end, $contig_id,
+ $chr_start, $chr_end, $chr_name, $contig_ori );
+
+
+ my @coordlist = $mapper->map_coordinates(2,5,-1,627012,"rawcontig");
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 AUTHOR - Ewan Birney
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Email birney@ebi.ac.uk
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Mapper;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+
+use Bio::Root::RootI;
+use Bio::EnsEMBL::Mapper::Pair;
+use Bio::EnsEMBL::Mapper::Unit;
+use Bio::EnsEMBL::Mapper::Coordinate;
+use Bio::EnsEMBL::Mapper::Gap;
+
+@ISA = qw(Bio::Root::RootI);
+
+# new() is written here
+
+sub new {
+ my($class,@args) = @_;
+
+ my $to = shift @args;
+ my $from = shift @args;
+
+ my $self = {};
+ bless $self,$class;
+
+ $self->{'_pair_hash_to'} = {};
+ $self->{'_pair_hash_from'} = {};
+
+ $self->to($to);
+ $self->from($from);
+
+# set stuff in self from @args
+ return $self;
+}
+
+
+=head2 map_coordinates
+
+ Title : map_coordinates
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub map_coordinates{
+ my ($self,$start,$end,$strand,$id,$type) = @_;
+
+ if( !defined $type ) {
+ $self->throw("Must start,end,strand,id,type as coordinates");
+ }
+
+ my $self_func;
+ my $target_func;
+ my $hash;
+
+ if( $type eq $self->to ) {
+ $self_func = \&Bio::EnsEMBL::Mapper::Pair::to;
+ $target_func = \&Bio::EnsEMBL::Mapper::Pair::from;
+ $hash = $self->{'_pair_hash_to'};
+ } elsif ( $type eq $self->from ) {
+ $self_func = \&Bio::EnsEMBL::Mapper::Pair::from;
+ $target_func = \&Bio::EnsEMBL::Mapper::Pair::to;
+ $hash = $self->{'_pair_hash_from'};
+ } else {
+ $self->throw("Type $type is neither to or from coordinate systems");
+ }
+
+ if( $self->_is_frozen == 0 ) {
+ $self->_freeze();
+ }
+
+ if( !defined $hash->{$id} ) {
+ # one big gap!
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new();
+ $gap->start($start);
+ $gap->end($end);
+ return $gap;
+ }
+
+ my $last_used_pair;
+ my @result;
+
+ foreach my $pair ( @{$hash->{$id}} ) {
+
+
+
+ my $self_coord = &$self_func($pair);
+ my $target_coord = &$target_func($pair);
+
+ # if we haven't even reached the start, move on
+ if( $self_coord->end < $start ) {
+ next;
+ }
+
+ # if we have over run, break
+ if( $self_coord->start > $end ) {
+ last;
+ }
+
+
+
+ if( $start < $self_coord->start ) {
+ # gap detected
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new();
+ $gap->start($start);
+ $gap->end($self_coord->start-1);
+ push(@result,$gap);
+ }
+
+ my ($target_start,$target_end,$target_ori);
+
+ # start is somewhere inside the region
+ if( $pair->ori == 1 ) {
+ $target_start = $target_coord->start + ($start - $self_coord->start);
+ } else {
+ $target_end = $target_coord->end - ($start - $self_coord->start);
+ }
+
+ # either we are enveloping this map or not. If yes, then end
+ # point (self perspective) is determined solely by target. If not
+ # we need to adjust
+
+ if( $end > $self_coord->end ) {
+ # enveloped
+ if( $pair->ori == 1 ) {
+ $target_end = $target_coord->end;
+ } else {
+ $target_start = $target_coord->start;
+ }
+ } else {
+ # need to adjust end
+ if( $pair->ori == 1 ) {
+ $target_end = $target_coord->start + ($end - $self_coord->start);
+ } else {
+ $target_start = $target_coord->end - ($end - $self_coord->start);
+ }
+ }
+
+ my $res = Bio::EnsEMBL::Mapper::Coordinate->new();
+ $res->start($target_start);
+ $res->end($target_end);
+ $res->strand($pair->ori * $strand);
+ $res->id($target_coord->id);
+ push(@result,$res);
+
+ $last_used_pair = $pair;
+ $start = $self_coord->end+1;
+ }
+
+
+ if( !defined $last_used_pair ) {
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new();
+ $gap->start($start);
+ $gap->end($end);
+ push(@result,$gap);
+
+ } elsif( &$self_func($last_used_pair)->end < $end ) {
+ # gap at the end
+ my $gap = Bio::EnsEMBL::Mapper::Gap->new();
+ $gap->start(&$self_func($last_used_pair)->end+1);
+ $gap->end($end);
+ push(@result,$gap);
+ }
+
+ if ( $strand == -1 ) {
+ @result = reverse ( @result);
+ }
+
+ return @result;
+
+}
+
+=head2 add_map_coordinates
+
+ Title : add_map_coordinates
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub add_map_coordinates{
+ my ($self,$contig_start,$contig_end,$contig_id,$chr_start,$chr_end,$chr_name,$contig_ori) = @_;
+
+ if( $contig_start !~ /\d+/ || $chr_start !~ /\d+/ ) {
+ $self->throw("Not doable - $contig_start as start or $chr_start as start?");
+ }
+
+ if( ($contig_end - $contig_start) != ($chr_end - $chr_start) ) {
+ $self->throw("Cannot deal with mis-lengthed mappings so far");
+ }
+
+ my $pair = Bio::EnsEMBL::Mapper::Pair->new();
+
+ my $from = Bio::EnsEMBL::Mapper::Unit->new();
+ $from->start($contig_start);
+ $from->end($contig_end);
+ $from->id($contig_id);
+
+ my $to = Bio::EnsEMBL::Mapper::Unit->new();
+ $to->start($chr_start);
+ $to->end($chr_end);
+ $to->id($chr_name);
+
+ $pair->to($to);
+ $pair->from($from);
+
+ $pair->ori($contig_ori);
+
+ # place into hash on both ids
+
+ if( !defined $self->{'_pair_hash_to'}->{$chr_name} ) {
+ $self->{'_pair_hash_to'}->{$chr_name} = [];
+ }
+ push(@{$self->{'_pair_hash_to'}->{$chr_name}},$pair);
+
+ if( !defined $self->{'_pair_hash_from'}->{$contig_id} ) {
+ $self->{'_pair_hash_from'}->{$contig_id} = [];
+ }
+ push(@{$self->{'_pair_hash_from'}->{$contig_id}},$pair);
+
+ $self->_is_frozen(0);
+}
+
+=head2 to
+
+ Title : to
+ Usage : $obj->to($newval)
+ Function:
+ Example :
+ Returns : value of to
+ Args : newvalue (optional)
+
+
+=cut
+
+sub to{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'to'} = $value;
+ }
+ return $self->{'to'};
+
+}
+
+=head2 from
+
+ Title : from
+ Usage : $obj->from($newval)
+ Function:
+ Example :
+ Returns : value of from
+ Args : newvalue (optional)
+
+
+=cut
+
+sub from{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'from'} = $value;
+ }
+ return $self->{'from'};
+
+}
+
+
+=head2 _dump
+
+ Title : _dump
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub _dump{
+ my ($self,$fh) = @_;
+
+ if( !defined $fh ) {
+ $fh = \*STDERR;
+ }
+
+ foreach my $id ( keys %{$self->{'_pair_hash_from'}} ) {
+ print $fh "From Hash $id\n";
+ foreach my $pair ( @{$self->{'_pair_hash_from'}->{$id}} ) {
+ print $fh " ",$pair->from->start," ",$pair->from->end,":",$pair->to->start," ",$pair->to->end," ",$pair->to->id,"\n";
+ }
+ }
+
+}
+
+
+=head2 _freeze
+
+ Title : _freeze
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub _freeze{
+ my ($self) = @_;
+
+ foreach my $id ( keys %{$self->{'_pair_hash_from'}} ) {
+ @{$self->{'_pair_hash_from'}->{$id}} = sort { $a->from->start <=> $b->from->start } @{$self->{'_pair_hash_from'}->{$id}};
+ }
+
+ foreach my $id ( keys %{$self->{'_pair_hash_to'}} ) {
+ @{$self->{'_pair_hash_to'}->{$id}} = sort { $a->to->start <=> $b->to->start } @{$self->{'_pair_hash_to'}->{$id}};
+ }
+
+ $self->_is_frozen(1);
+
+}
+
+
+
+=head2 _is_frozen
+
+ Title : _is_frozen
+ Usage : $obj->_is_frozen($newval)
+ Function:
+ Example :
+ Returns : value of _is_frozen
+ Args : newvalue (optional)
+
+
+=cut
+
+sub _is_frozen{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'_is_frozen'} = $value;
+ }
+ return $self->{'_is_frozen'};
+
+}
+
+
+
+
+
+
+
+
diff --git a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
new file mode 100644
index 0000000000000000000000000000000000000000..b2c17900b3e3ce396cd8e0fd1a106f441ced9d5b
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
@@ -0,0 +1,143 @@
+
+#
+# Ensembl module for Bio::EnsEMBL::MapperCoordinate
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright GRL and EBI
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper::Coordinate - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 CONTACT
+
+Ensembl - ensembl-dev@ebi.ac.uk
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Mapper::Coordinate;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inheriets from Bio::Root::RootI
+
+use Bio::Root::RootI;
+
+
+@ISA = qw(Bio::Root::RootI);
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = {};
+ bless $self,$class;
+
+ return $self;
+}
+
+=head2 start
+
+ Title : start
+ Usage : $obj->start($newval)
+ Function:
+ Returns : value of start
+ Args : newvalue (optional)
+
+
+=cut
+
+sub start{
+ my $obj = shift;
+ if( @_ ) {
+ my $value = shift;
+ $obj->{'start'} = $value;
+ }
+ return $obj->{'start'};
+
+}
+
+=head2 end
+
+ Title : end
+ Usage : $obj->end($newval)
+ Function:
+ Returns : value of end
+ Args : newvalue (optional)
+
+
+=cut
+
+sub end{
+ my $obj = shift;
+ if( @_ ) {
+ my $value = shift;
+ $obj->{'end'} = $value;
+ }
+ return $obj->{'end'};
+
+}
+
+=head2 strand
+
+ Title : strand
+ Usage : $obj->strand($newval)
+ Function:
+ Returns : value of strand
+ Args : newvalue (optional)
+
+
+=cut
+
+sub strand{
+ my $obj = shift;
+ if( @_ ) {
+ my $value = shift;
+ $obj->{'strand'} = $value;
+ }
+ return $obj->{'strand'};
+
+}
+
+=head2 id
+
+ Title : id
+ Usage : $obj->id($newval)
+ Function:
+ Example :
+ Returns : value of id
+ Args : newvalue (optional)
+
+
+=cut
+
+sub id{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'id'} = $value;
+ }
+ return $self->{'id'};
+
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Mapper/Gap.pm b/modules/Bio/EnsEMBL/Mapper/Gap.pm
new file mode 100644
index 0000000000000000000000000000000000000000..9ee3615e37a5dd65d7b475bd15188ee7e49469a3
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Mapper/Gap.pm
@@ -0,0 +1,108 @@
+
+
+#
+# Ensembl module for Bio::EnsEMBL::Mapper::Gap
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper::Gap - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 AUTHOR - Ewan Birney
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Email birney@ebi.ac.uk
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Mapper::Gap;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+# new() is written here
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = {};
+ bless $self,$class;
+
+# set stuff in self from @args
+ return $self;
+}
+
+=head2 start
+
+ Title : start
+ Usage : $obj->start($newval)
+ Function:
+ Example :
+ Returns : value of start
+ Args : newvalue (optional)
+
+
+=cut
+
+sub start{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'start'} = $value;
+ }
+ return $self->{'start'};
+
+}
+
+=head2 end
+
+ Title : end
+ Usage : $obj->end($newval)
+ Function:
+ Example :
+ Returns : value of end
+ Args : newvalue (optional)
+
+
+=cut
+
+sub end{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'end'} = $value;
+ }
+ return $self->{'end'};
+
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Mapper/Pair.pm b/modules/Bio/EnsEMBL/Mapper/Pair.pm
new file mode 100644
index 0000000000000000000000000000000000000000..10e6da10a27300fece42a72e9317034e8d97c7a4
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Mapper/Pair.pm
@@ -0,0 +1,128 @@
+
+#
+# Ensembl module for Bio::EnsEMBL::Mapper::Pair
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper::Pair - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 AUTHOR - Ewan Birney
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Email birney@ebi.ac.uk
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Mapper::Pair;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+# new() is written here
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = {};
+ bless $self,$class;
+
+# set stuff in self from @args
+ return $self;
+}
+
+=head2 to
+
+ Title : to
+ Usage : $obj->to($newval)
+ Function:
+ Example :
+ Returns : value of to
+ Args : newvalue (optional)
+
+
+=cut
+
+sub to{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'to'} = $value;
+ }
+ return $self->{'to'};
+
+}
+
+=head2 from
+
+ Title : from
+ Usage : $obj->from($newval)
+ Function:
+ Example :
+ Returns : value of from
+ Args : newvalue (optional)
+
+
+=cut
+
+sub from{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'from'} = $value;
+ }
+ return $self->{'from'};
+
+}
+
+=head2 ori
+
+ Title : ori
+ Usage : $obj->ori($newval)
+ Function:
+ Example :
+ Returns : value of ori
+ Args : newvalue (optional)
+
+
+=cut
+
+sub ori{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'ori'} = $value;
+ }
+ return $self->{'ori'};
+
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Mapper/Unit.pm b/modules/Bio/EnsEMBL/Mapper/Unit.pm
new file mode 100644
index 0000000000000000000000000000000000000000..754d0f113773d02a5d67cba313a0b35dfe76142b
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Mapper/Unit.pm
@@ -0,0 +1,129 @@
+
+#
+# Ensembl module for Bio::EnsEMBL::Mapper::Unit
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Mapper::Unit - One side of a map pair
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 AUTHOR - Ewan Birney
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Email birney@ebi.ac.uk
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Mapper::Unit;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+# new() is written here
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = {};
+ bless $self,$class;
+
+# set stuff in self from @args
+ return $self;
+}
+
+=head2 id
+
+ Title : id
+ Usage : $obj->id($newval)
+ Function:
+ Example :
+ Returns : value of id
+ Args : newvalue (optional)
+
+
+=cut
+
+sub id{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'id'} = $value;
+ }
+ return $self->{'id'};
+
+}
+
+=head2 start
+
+ Title : start
+ Usage : $obj->start($newval)
+ Function:
+ Example :
+ Returns : value of start
+ Args : newvalue (optional)
+
+
+=cut
+
+sub start{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'start'} = $value;
+ }
+ return $self->{'start'};
+
+}
+
+=head2 end
+
+ Title : end
+ Usage : $obj->end($newval)
+ Function:
+ Example :
+ Returns : value of end
+ Args : newvalue (optional)
+
+
+=cut
+
+sub end{
+ my ($self,$value) = @_;
+ if( defined $value) {
+ $self->{'end'} = $value;
+ }
+ return $self->{'end'};
+
+}
+
+
+1;
diff --git a/modules/t/mapper.t b/modules/t/mapper.t
index e96e32876dc17dd8179a5e1a5cb155251ab0f76c..5ee3bb02bfd521b3500cdfeb749767b0aa7a93a7 100644
--- a/modules/t/mapper.t
+++ b/modules/t/mapper.t
@@ -21,7 +21,7 @@
## We start with some black magic to print on failure.
-BEGIN { $| = 1; print "1..4\n";
+BEGIN { $| = 1; print "1..6\n";
use vars qw($loaded); }
END {print "not ok 1\n" unless $loaded;}
@@ -30,13 +30,16 @@ use lib 't';
$loaded = 1;
print "ok 1\n"; # 1st test passes.
-
+
+use Bio::EnsEMBL::Mapper;
# testing the Bio::EnsEMBL::Mapper module
-$map = Bio::EnsEMBL::Mapper->new( "virtualcontig", "rawcontig" );
-load_sgp_dump( $map );
+$mapper = Bio::EnsEMBL::Mapper->new( "virtualcontig", "rawcontig" );
+load_sgp_dump( $mapper );
+$mapper->_freeze;
+#$mapper->_dump;
# loading done successfully
print "ok 2\n";
@@ -50,37 +53,45 @@ if( @coordlist == 1 ) {
print "not ok 3\n";
}
-if( $coordlist[0]->{'start'} == 2 &&
- $coordlist[0]->{'end' } == 5 &&
- $coordlist[0]->{'strand' } == -1 ) {
+if( $coordlist[0]->start == 2 &&
+ $coordlist[0]->end == 5 &&
+ $coordlist[0]->strand == -1 ) {
print "ok 4\n";
} else {
print "not ok 4\n";
- print STDERR %$coordlist[0];
}
# now a split coord
-@coordlist = $map->map_coordinates( 383700, 444000, 1, "chr1", "virtualcontig" );
+@coordlist = $mapper->map_coordinates( 383700, 444000, 1, "chr1", "virtualcontig" );
# should be ( 56072, 56092, -1, 314696 )
# (about:-) ( 126, 59773, -1, 341 )
# ( 5332, 5963, -1, 315843)
-if( @coordlist = 3 ) {
+if( scalar(@coordlist) == 3 ) {
print "ok 5\n";
} else {
print "not ok 5\n";
}
+if( $coordlist[0]->start == 31917 &&
+ $coordlist[0]->end == 31937 &&
+ $coordlist[0]->id == 314696 &&
+ $coordlist[0]->strand == -1 ) {
+ print "ok 6\n";
+} else {
+ print "not ok 6\n";
+}
+
sub load_sgp_dump {
my $map = shift;
+#chr_name raw_id chr_start chr_end raw_start raw_end raw_ori
my @sgp_dump = split ( /\n/, qq {
-chr_name raw_id chr_start chr_end raw_start raw_end raw_ori
chr1 627012 1 31276 1 31276 1
chr1 627010 31377 42949 72250 83822 -1
chr1 2768 42950 180950 251 138251 1
@@ -198,3 +209,4 @@ chr1 625359 1214016 1216330 1 2315 1
}
+