diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
index da53bb7e39120527fcf5059177245ccb99750868..14fe5166f0799bbc59c5e6e8e1e884ed7589649a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
@@ -364,55 +364,54 @@ sub _remap {
type and alternate_slice) of if $asx not a Bio::EnsEMBL::AssemblyException
Caller: general
Status: Stable
-=cut
-# use Data::Dumper;
+=cut
sub store{
- my $self = shift;
- my $asx = shift;
- my $asx2 = shift;
+ my $self = shift;
+ my $asx = shift;
+ my $asx2 = shift;
- if (! $asx->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
- throw("$asx is not a Ensembl assemlby exception -- not stored");
- }
- #if already present, return ID in the database
- my $db = $self->db();
- if ($asx->is_stored($db)){
- return $asx->dbID();
- }
- #do some checkings for the object
- #at the moment, the orientation is always 1
- if (! $asx->start || ! $asx->end ){
- throw("Assembly exception does not have coordinates");
- }
- if ($asx->type !~ /PAR|HAP/){
- throw("Only types of assembly exception features valid are PAR and HAP");
- }
- if ( !($asx->alternate_slice->isa('Bio::EnsEMBL::Slice') or $asx->alternate_slice->isa('Bio::EnsEMBL::LRGSlice')) ){
- throw("Alternate slice should be a Bio::EnsEMBL::Slice");
- }
- #now check the other Assembly exception feature, the one pointing to the REF
- # region
- if (!$asx2->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
- throw("$asx2 is not a Ensembl assemlby exception -- not stored");
- }
- if (! $asx2->start || ! $asx2->end ){
- throw("Assembly exception does not have coordinates");
- }
- if ($asx2->type !~ /HAP REF|PAR REF/){
- throw("$asx2 should have type of assembly exception features HAP REF or PAR REF");
- }
- if (! ($asx2->alternate_slice->isa('Bio::EnsEMBL::Slice') or $asx2->alternate_slice->isa('Bio::EnsEMBL::LRGSlice'))){
- throw("Alternate slice should be a Bio::EnsEMBL::Slice");
- }
- #finally check that both features are pointing to each other slice
- if ($asx->slice != $asx2->alternate_slice || $asx->alternate_slice != $asx2->slice){
- throw("Slice and alternate slice in both features are not pointing to each other");
- }
- #prepare the SQL
- my $asx_sql = q{
+ if (! $asx->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
+ throw("$asx is not a Ensembl assemlby exception -- not stored");
+ }
+ #if already present, return ID in the database
+ my $db = $self->db();
+ if ($asx->is_stored($db)){
+ return $asx->dbID();
+ }
+ #do some checkings for the object
+ #at the moment, the orientation is always 1
+ if (! $asx->start || ! $asx->end ){
+ throw("Assembly exception does not have coordinates");
+ }
+ if ($asx->type !~ /PAR|HAP|PATCH_NOVEL|PATCH_FIX/){
+ throw("Only types of assembly exception features valid are PAR, HAP, PATCH_FIX or PATCH_NOVEL");
+ }
+ if ( !($asx->alternate_slice->isa('Bio::EnsEMBL::Slice')) ){
+ throw("Alternate slice should be a Bio::EnsEMBL::Slice");
+ }
+ #now check the other Assembly exception feature, the one pointing to the REF
+ # region
+ if (!$asx2->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
+ throw("$asx2 is not a Ensembl assemlby exception -- not stored");
+ }
+ if (! $asx2->start || ! $asx2->end ){
+ throw("Assembly exception does not have coordinates");
+ }
+ if ($asx2->type !~ /HAP REF|PAR REF|PATCH_NOVEL REF|PATCH_FIX REF/){
+ throw("$asx2 should have type of assembly exception features HAP REF, PAR REF, PATCH_FIX REF or PATCH_NOVEL REF");
+ }
+ if (! ($asx2->alternate_slice->isa('Bio::EnsEMBL::Slice')) ){
+ throw("Alternate slice should be a Bio::EnsEMBL::Slice");
+ }
+ #finally check that both features are pointing to each other slice
+ if ($asx->slice != $asx2->alternate_slice || $asx->alternate_slice != $asx2->slice){
+ throw("Slice and alternate slice in both features are not pointing to each other");
+ }
+ #prepare the SQL
+ my $asx_sql = q{
INSERT INTO assembly_exception( seq_region_id, seq_region_start,
seq_region_end,
exc_type, exc_seq_region_id,
@@ -420,41 +419,41 @@ sub store{
ori)
VALUES (?, ?, ?, ?, ?, ?, ?, 1)
};
-
- my $asx_st = $self->prepare($asx_sql);
- my $asx_id = undef;
- my $asx_seq_region_id;
- my $asx2_seq_region_id;
- my $original = $asx;
- my $original2 = $asx2;
- #check all feature information
- ($asx, $asx_seq_region_id) = $self->_pre_store($asx);
- ($asx2, $asx2_seq_region_id) = $self->_pre_store($asx2);
-
- #and store it
- $asx_st->bind_param(1, $asx_seq_region_id, SQL_INTEGER);
- $asx_st->bind_param(2, $asx->start(), SQL_INTEGER);
- $asx_st->bind_param(3, $asx->end(), SQL_INTEGER);
- $asx_st->bind_param(4, $asx->type(), SQL_VARCHAR);
- $asx_st->bind_param(5, $asx2_seq_region_id, SQL_INTEGER);
- $asx_st->bind_param(6, $asx2->start(), SQL_INTEGER);
- $asx_st->bind_param(7, $asx2->end(), SQL_INTEGER);
-
- $asx_st->execute();
- $asx_id = $asx_st->{'mysql_insertid'};
-
- #finally, update the dbID and adaptor of the asx and asx2
- $original->adaptor($self);
- $original->dbID($asx_id);
- $original2->adaptor($self);
- $original2->dbID($asx_id);
- #and finally update dbID cache with new assembly exception
- $self->{'_aexc_dbID_cache'}->{$asx_id} = $original;
- #and update the other caches as well
- push @{$self->{'_aexc_slice_cache'}->{uc($asx->slice->name)}},$original, $original2;
- push @{$self->{'_aexc_cache'}}, $original, $original2;
-
- return $asx_id;
+
+ my $asx_st = $self->prepare($asx_sql);
+ my $asx_id = undef;
+ my $asx_seq_region_id;
+ my $asx2_seq_region_id;
+ my $original = $asx;
+ my $original2 = $asx2;
+ #check all feature information
+ ($asx, $asx_seq_region_id) = $self->_pre_store($asx);
+ ($asx2, $asx2_seq_region_id) = $self->_pre_store($asx2);
+
+ #and store it
+ $asx_st->bind_param(1, $asx_seq_region_id, SQL_INTEGER);
+ $asx_st->bind_param(2, $asx->start(), SQL_INTEGER);
+ $asx_st->bind_param(3, $asx->end(), SQL_INTEGER);
+ $asx_st->bind_param(4, $asx->type(), SQL_VARCHAR);
+ $asx_st->bind_param(5, $asx2_seq_region_id, SQL_INTEGER);
+ $asx_st->bind_param(6, $asx2->start(), SQL_INTEGER);
+ $asx_st->bind_param(7, $asx2->end(), SQL_INTEGER);
+
+ $asx_st->execute();
+ $asx_id = $asx_st->{'mysql_insertid'};
+
+ #finally, update the dbID and adaptor of the asx and asx2
+ $original->adaptor($self);
+ $original->dbID($asx_id);
+ $original2->adaptor($self);
+ $original2->dbID($asx_id);
+ #and finally update dbID cache with new assembly exception
+ $self->{'_aexc_dbID_cache'}->{$asx_id} = $original;
+ #and update the other caches as well
+ push @{$self->{'_aexc_slice_cache'}->{uc($asx->slice->name)}},$original, $original2;
+ push @{$self->{'_aexc_cache'}}, $original, $original2;
+
+ return $asx_id;
}
#
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index 49d9138c89bb1e024a9d70b6036d48047c80d6b8..0f1a393aca4715018bdc3da4a35a2d196178317d 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -1096,9 +1096,11 @@ sub get_all_alt_locations {
push @haps, $axf;
} elsif(uc($axf->type()) =~ 'PAR') {
push @alt, $axf;
- } elsif( $axf->type() eq "HAP REF" ) {
- push @haps, $axf if $return_all > 0 ;
- # do nothing when you are on REF
+ } elsif( $axf->type() eq "PATCH_FIX"){
+# } elsif( $axf->type() eq "HAP REF" ) {
+# push @haps, $axf if $return_all > 0 ;
+# # do nothing when you are on REF
+ } elsif( $axf->type() eq "PATCH_NOVEL"){
} else {
warning("Unknown exception feature type ". $axf->type()."- ignoring.");
}