diff --git a/modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm
new file mode 100644
index 0000000000000000000000000000000000000000..e4d860edcf411837c14b4b9d3769775df5c8ac40
--- /dev/null
+++ b/modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm
@@ -0,0 +1,469 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::SlicingEventAdaptor - Database adaptor for the retrieval and
+storage of SplicingEvent objects
+
+=head1 SYNOPSIS
+
+ use Bio::EnsEMBL::Registry;
+
+ Bio::EnsEMBL::Registry->load_registry_from_db(
+ -host => 'ensembldb.ensembl.org',
+ -user => 'anonymous',
+ );
+
+ $se_adaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEvent" );
+
+ $se = $se_adaptor->fetch_by_dbID(12);
+
+ @ses = $se_adaptor->fetch_by_stable_id('ENSG00000184129');
+
+ @sess = @{ $se_adaptor->fetch_by__name('...-CNE-1') };
+
+ $slice_adaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
+
+ $slice =
+ $slice_adaptor->fetch_by_region( 'chromosome', '1', 1, 1000000 );
+
+ @ase = @{ $se_adaptor->fetch_all_by_Slice($slice) };
+
+=head1 DESCRIPTION
+
+This is a database aware adaptor for the retrieval and storage ofSlicingEvents
+objects.
+
+=head1 METHODS
+
+=cut
+package Bio::EnsEMBL::DBSQL::SplicingEventAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::SplicingEvent;
+
+use vars '@ISA';
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+
+
+=head2 list_dbIDs
+
+ Example : @gene_ids = @{$gene_adaptor->list_dbIDs()};
+ Description: Gets an array of internal ids for all genes in the current db
+ Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
+ Returntype : Listref of Ints
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub list_dbIDs {
+ my ($self,$ordered) = @_;
+
+ return $self->_list_dbIDs("splicing_event", undef, $ordered);
+}
+
+
+=head2 fetch_all_by_Slice
+
+ Arg [1] : Bio::EnsEMBL::Slice $slice
+ The slice to fetch genes on.
+ Arg [2] : type of Transcript event
+ Arg [3] : (optional) boolean $load_features
+ if true, transcript will be loaded immediately rather than
+ lazy loaded later.
+=cut
+
+sub fetch_all_by_Slice{
+ my $self = shift;
+ my $slice = shift;
+ my $type = shift;
+ my $load_features = shift;
+
+ my $constraint = "";
+
+ if(defined($type)){
+ $constraint .= " and se.type = '$type'";
+ }
+
+ my $tes = $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
+
+
+ # Is there any use in having a splice event without the paris and features??
+
+
+ if(!$load_features || @$tes < 2) {
+ return $tes;
+ }
+
+ ## do someother stuff..
+
+ foreach my $te (@$tes){
+ $te->get_all_Features();
+ $te->get_all_Pairs();
+ }
+
+ return $tes;
+}
+
+
+
+
+
+sub fetch_all_by_Gene{
+ my $self = shift;
+ my $gene = shift;
+
+ my ($splicing_event_id,$seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $name, $gene_id, $type);
+
+ my $sth = $self->dbc->prepare("select se.splicing_event_id , se.seq_region_id, se.seq_region_start, se.seq_region_end, se.seq_region_strand, se.name, se.type from splicing_event se where se.gene_id = ".$gene->dbID);
+
+ $sth->execute();
+
+ $sth->bind_columns(\$splicing_event_id, \$seq_region_id, \$seq_region_start, \$seq_region_end, \$seq_region_strand, \$name, \$type);
+
+ my @splicing_events;
+
+ my $sa = $self->db->get_SliceAdaptor();
+
+ while($sth->fetch){
+
+ my $slice = $sa->fetch_by_seq_region_id($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand);
+
+ push( @splicing_events,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
+ 'start' => $seq_region_start,
+ 'end' => $seq_region_end,
+ 'strand' => $seq_region_strand,
+ 'adaptor' => $self,
+ 'slice' => $slice,
+ 'dbID' => $splicing_event_id,
+ 'name' => $name,
+ 'gene_id' => $gene->dbID,
+ 'type' => $type
+ } ) );
+ }
+ $sth->finish;
+
+ foreach my $te (@splicing_events){
+ $te->get_all_Features();
+ $te->get_all_Pairs();
+ }
+ return \@splicing_events;
+}
+
+sub fetch_all_by_Exon{
+ my $self = shift;
+ my $exon = shift;
+
+ my $list = "(";
+ my $sth= $self->dbc->prepare("Select distinct(splicing_event_id) from splicing_event_feature where exon_id = ".$exon->dbID);
+ $sth->execute;
+ my ($se_id);
+ $sth->bind_columns(\$se_id);
+ while($sth->fetch){
+ $list .= $se_id." ,";
+ }
+ $sth->finish;
+ chop $list; # get rid of last ","
+ $list .= ")";
+
+ my ($splicing_event_id,$seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $name, $gene_id, $type);
+
+ $sth = $self->dbc->prepare("select se.splicing_event_id , se.seq_region_id, se.seq_region_start, se.seq_region_end, se.seq_region_strand, se.name, se.type, se.gene_id from splicing_event se where se.splicing_event_id in ".$list);
+
+ $sth->execute();
+
+ $sth->bind_columns(\$splicing_event_id, \$seq_region_id, \$seq_region_start, \$seq_region_end, \$seq_region_strand, \$name, \$type, \$gene_id);
+
+ my @splicing_events;
+
+ my $sa = $self->db->get_SliceAdaptor();
+
+ while($sth->fetch){
+
+ my $slice = $sa->fetch_by_seq_region_id($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand);
+
+ push( @splicing_events,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
+ 'start' => $seq_region_start,
+ 'end' => $seq_region_end,
+ 'strand' => $seq_region_strand,
+ 'adaptor' => $self,
+ 'slice' => $slice,
+ 'dbID' => $splicing_event_id,
+ 'name' => $name,
+ 'gene_id' => $gene_id,
+ 'type' => $type
+ } ) );
+ }
+ $sth->finish;
+
+ foreach my $te (@splicing_events){
+ $te->get_all_Features();
+ $te->get_all_Pairs();
+ }
+ return \@splicing_events;
+}
+
+sub fetch_all_by_Transcript{
+ my $self = shift;
+ my $tran = shift;
+
+ my $list = "(";
+ my $sth= $self->dbc->prepare("Select distinct(splicing_event_id) from splicing_event_feature where transcript_id = ".$tran->dbID);
+ $sth->execute;
+ my ($se_id);
+ $sth->bind_columns(\$se_id);
+ while($sth->fetch){
+ $list .= $se_id." ,";
+ }
+ $sth->finish;
+ chop $list; # get rid of last ","
+ $list .= ")";
+
+ my ($splicing_event_id,$seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $name, $gene_id, $type);
+
+ $sth = $self->dbc->prepare("select se.splicing_event_id , se.seq_region_id, se.seq_region_start, se.seq_region_end, se.seq_region_strand, se.name, se.type, se.gene_id from splicing_event se where se.splicing_event_id in ".$list);
+
+ $sth->execute();
+
+ $sth->bind_columns(\$splicing_event_id, \$seq_region_id, \$seq_region_start, \$seq_region_end, \$seq_region_strand, \$name, \$type, \$gene_id);
+
+ my @splicing_events;
+
+ my $sa = $self->db->get_SliceAdaptor();
+
+ while($sth->fetch){
+
+ my $slice = $sa->fetch_by_seq_region_id($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand);
+
+ push( @splicing_events,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
+ 'start' => $seq_region_start,
+ 'end' => $seq_region_end,
+ 'strand' => $seq_region_strand,
+ 'adaptor' => $self,
+ 'slice' => $slice,
+ 'dbID' => $splicing_event_id,
+ 'name' => $name,
+ 'gene_id' => $gene_id,
+ 'type' => $type
+ } ) );
+ }
+ $sth->finish;
+
+ foreach my $te (@splicing_events){
+ $te->get_all_Features();
+ $te->get_all_Pairs();
+ }
+ return \@splicing_events;
+}
+
+# _tables
+# Arg [1] : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns the names, aliases of the tables to use for queries.
+# Returntype : list of listrefs of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _tables {
+ my $self = shift;
+
+ return ([ 'splicing_event', 'se' ]);
+}
+
+# _columns
+# Arg [1] : none
+# Example : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns a list of columns to use for queries.
+# Returntype : list of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _columns {
+ my $self = shift;
+
+# my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
+# my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
+
+ return ( 'se.splicing_event_id', 'se.seq_region_id', 'se.seq_region_start', 'se.seq_region_end', 'se.seq_region_strand', 'se.name', 'se.gene_id', 'se.type' );
+
+}
+
+sub _objs_from_sth {
+ my ($self, $sth, $mapper, $dest_slice) = @_;
+
+ my ($splicing_event_id,$seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $name, $gene_id, $type);
+
+
+ $sth->bind_columns(\$splicing_event_id, \$seq_region_id, \$seq_region_start, \$seq_region_end, \$seq_region_strand, \$name, \$gene_id, \$type);
+
+ my $sa = $self->db()->get_SliceAdaptor();
+
+
+ my @splicing_events;
+ my %slice_hash;
+ my %sr_name_hash;
+ my %sr_cs_hash;
+
+ my $asm_cs;
+ my $cmp_cs;
+ my $asm_cs_vers;
+ my $asm_cs_name;
+ my $cmp_cs_vers;
+ my $cmp_cs_name;
+ if($mapper) {
+ $asm_cs = $mapper->assembled_CoordSystem();
+ $cmp_cs = $mapper->component_CoordSystem();
+ $asm_cs_name = $asm_cs->name();
+ $asm_cs_vers = $asm_cs->version();
+ $cmp_cs_name = $cmp_cs->name();
+ $cmp_cs_vers = $cmp_cs->version();
+ }
+
+ my $dest_slice_start;
+ my $dest_slice_end;
+ my $dest_slice_strand;
+ my $dest_slice_length;
+ my $dest_slice_cs;
+ my $dest_slice_sr_name;
+ my $dest_slice_sr_id;
+ my $asma;
+ if($dest_slice) {
+ $dest_slice_start = $dest_slice->start();
+ $dest_slice_end = $dest_slice->end();
+ $dest_slice_strand = $dest_slice->strand();
+ $dest_slice_length = $dest_slice->length();
+ $dest_slice_cs = $dest_slice->coord_system();
+ $dest_slice_sr_name = $dest_slice->seq_region_name();
+ $dest_slice_sr_id = $dest_slice->get_seq_region_id();
+ $asma = $self->db->get_AssemblyMapperAdaptor();
+ }
+
+ FEATURE: while($sth->fetch()) {
+ #need to get the internal_seq_region, if present
+ $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
+
+ my $slice = $slice_hash{"ID:".$seq_region_id};
+ my $dest_mapper = $mapper;
+
+ if(!$slice) {
+ $slice = $sa->fetch_by_seq_region_id($seq_region_id);
+ $slice_hash{"ID:".$seq_region_id} = $slice;
+ $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
+ $sr_cs_hash{$seq_region_id} = $slice->coord_system();
+ }
+
+ #obtain a mapper if none was defined, but a dest_seq_region was
+ if(!$dest_mapper && $dest_slice &&
+ !$dest_slice_cs->equals($slice->coord_system)) {
+ $dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs,
+ $slice->coord_system);
+ $asm_cs = $dest_mapper->assembled_CoordSystem();
+ $cmp_cs = $dest_mapper->component_CoordSystem();
+ $asm_cs_name = $asm_cs->name();
+ $asm_cs_vers = $asm_cs->version();
+ $cmp_cs_name = $cmp_cs->name();
+ $cmp_cs_vers = $cmp_cs->version();
+ }
+
+ my $sr_name = $sr_name_hash{$seq_region_id};
+ my $sr_cs = $sr_cs_hash{$seq_region_id};
+ #
+ # remap the feature coordinates to another coord system
+ # if a mapper was provided
+ #
+ if($dest_mapper) {
+
+ ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
+ $dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
+ $seq_region_strand, $sr_cs);
+
+ #skip features that map to gaps or coord system boundaries
+ next FEATURE if(!defined($seq_region_id));
+
+ #get a slice in the coord system we just mapped to
+ $slice = $slice_hash{"ID:".$seq_region_id} ||=
+ $sa->fetch_by_seq_region_id($seq_region_id);
+ }
+
+ #
+ # If a destination slice was provided convert the coords
+ # If the dest_slice starts at 1 and is foward strand, nothing needs doing
+ #
+ if($dest_slice) {
+ if($dest_slice_start != 1 || $dest_slice_strand != 1) {
+ if($dest_slice_strand == 1) {
+ $seq_region_start = $seq_region_start - $dest_slice_start + 1;
+ $seq_region_end = $seq_region_end - $dest_slice_start + 1;
+ } else {
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start = $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
+ $seq_region_strand *= -1;
+ }
+ }
+
+ #throw away features off the end of the requested slice
+ if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
+ ( $dest_slice_sr_id != $seq_region_id )) {
+ next FEATURE;
+ }
+
+ $slice = $dest_slice;
+ }
+
+ # Finally, create the new splicing_event.
+ push( @splicing_events,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
+ 'start' => $seq_region_start,
+ 'end' => $seq_region_end,
+ 'strand' => $seq_region_strand,
+ 'adaptor' => $self,
+ 'slice' => $slice,
+ 'dbID' => $splicing_event_id,
+ 'name' => $name,
+ 'gene_id' => $gene_id,
+ 'type' => $type
+ } ) );
+
+ }
+
+ return \@splicing_events;
+}
+
+
+1;
+
+
diff --git a/modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm
new file mode 100644
index 0000000000000000000000000000000000000000..4da7adf42073cda1b4c3cc9bbd1c518d0d83b378
--- /dev/null
+++ b/modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm
@@ -0,0 +1,147 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::SlicingEventFeatureAdaptor - Database adaptor for the retrieval and
+storage of SplicingEventFeature objects
+
+=head1 SYNOPSIS
+
+ use Bio::EnsEMBL::Registry;
+
+ Bio::EnsEMBL::Registry->load_registry_from_db(
+ -host => 'ensembldb.ensembl.org',
+ -user => 'anonymous',
+ );
+
+ $se_adaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEventFeature" );
+
+
+=head1 DESCRIPTION
+
+This is a database aware adaptor for the retrieval and storage of SlicingEventFeatures
+objects.
+
+=head1 METHODS
+
+=cut
+package Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::SplicingEventFeature;
+
+use vars '@ISA';
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+
+
+
+sub fetch_all_by_SplicingEvent{
+ my ($self, $splicing_event) = @_;
+
+
+ my ($splicing_event_feature_id, $splicing_event_id, $exon_id, $transcript_id, $feature_order, $transcript_association, $type, $start, $end);
+
+ $splicing_event_id = $splicing_event->dbID;
+
+ my $sql = "select splicing_event_feature_id, exon_id, transcript_id, feature_order, transcript_association, type, start, end from splicing_event_feature where splicing_event_id = $splicing_event_id";
+
+ my $sth = $self->prepare($sql);
+
+ $sth->execute();
+ $sth->bind_columns(\$splicing_event_feature_id, \$exon_id, \$transcript_id, \$feature_order, \$transcript_association, \$type, \$start, \$end);
+
+ my @features;
+
+ while($sth->fetch()){
+ push( @features,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEventFeature', {
+ 'start' => $start,
+ 'end' => $end,
+ 'adaptor' => $self,
+ 'dbID' => $splicing_event_feature_id,
+ 'exon_id' => $exon_id,
+ 'transcript_id' => $transcript_id,
+ 'slice' => $splicing_event->slice,
+ 'type' => $type,
+ 'feature_order' => $feature_order,
+ 'transcript_association' => $transcript_association
+ } ) );
+
+ }
+ $sth->finish;
+ return \@features;
+
+}
+
+
+
+
+# _tables
+# Arg [1] : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns the names, aliases of the tables to use for queries.
+# Returntype : list of listrefs of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _tables {
+ my $self = shift;
+
+ return ([ 'splicing_event_feature', 'sef' ]);
+}
+
+# _columns
+# Arg [1] : none
+# Example : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns a list of columns to use for queries.
+# Returntype : list of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _columns {
+ my $self = shift;
+
+# my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
+# my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
+
+ return ( 'sef.splicing_event_id','sef.exon_id', 'sef.feature_order', 'sef.transcript_association', 'sef.type', 'sef.start', 'sef.end' );
+
+}
+
+sub list_dbIDs {
+ my ($self,$ordered) = @_;
+
+ return $self->_list_dbIDs("splicing_event_feature", undef, $ordered);
+}
+
+
+1;
+
+
diff --git a/modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm
new file mode 100644
index 0000000000000000000000000000000000000000..d52ff4769d04ba585776bde2e2d258d01b85a2d4
--- /dev/null
+++ b/modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm
@@ -0,0 +1,143 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::SlicingTranscriptPairAdaptor - Database adaptor for the retrieval and
+storage of SplicingTranscriptPair objects
+
+=head1 SYNOPSIS
+
+ use Bio::EnsEMBL::Registry;
+
+ Bio::EnsEMBL::Registry->load_registry_from_db(
+ -host => 'ensembldb.ensembl.org',
+ -user => 'anonymous',
+ );
+
+ $se_adaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingTranscriptPair" );
+
+
+=head1 DESCRIPTION
+
+This is a database aware adaptor for the retrieval and storage of SplicingTranscriptPairs
+objects.
+
+=head1 METHODS
+
+=cut
+package Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::SplicingTranscriptPair;
+
+use vars '@ISA';
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+
+
+
+sub fetch_all_by_SplicingEvent{
+ my ($self, $splicing_event) = @_;
+
+
+ my ($splicing_transcript_pair_id, $transcript_id_1, $transcript_id_2);
+
+ my $splicing_event_id = $splicing_event->dbID;
+
+ my $sql = "select splicing_transcript_pair_id, transcript_id_1, transcript_id_2 from splicing_transcript_pair where splicing_event_id = $splicing_event_id";
+
+ my $sth = $self->prepare($sql);
+
+ $sth->execute();
+ $sth->bind_columns(\$splicing_transcript_pair_id, \$transcript_id_1, \$transcript_id_2);
+
+ my @pairs;
+
+ while($sth->fetch()){
+ push( @pairs,
+ $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingTranscriptPair', {
+ 'adaptor' => $self,
+ 'dbID' => $splicing_transcript_pair_id,
+ 'transcript_id_1' => $transcript_id_1,
+ 'transcript_id_2' => $transcript_id_2,
+ 'start' => $splicing_event->start,
+ 'end' => $splicing_event->end
+ } ) );
+
+ }
+ $sth->finish;
+ return \@pairs;
+
+}
+
+
+
+
+# _tables
+# Arg [1] : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns the names, aliases of the tables to use for queries.
+# Returntype : list of listrefs of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _tables {
+ my $self = shift;
+
+ return ([ 'splicing_transcript_pair', 'stp' ]);
+}
+
+# _columns
+# Arg [1] : none
+# Example : none
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns a list of columns to use for queries.
+# Returntype : list of strings
+# Exceptions : none
+# Caller : internal
+# Status : At Risk
+
+sub _columns {
+ my $self = shift;
+
+# my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
+# my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
+
+ return ( 'stp.splicing_transcript_pair_id','stp.transcript_id_1', 'stp.transcript_id_2');
+
+}
+
+sub list_dbIDs {
+ my ($self,$ordered) = @_;
+
+ return $self->_list_dbIDs("splicing_transcript_pair", undef, $ordered);
+}
+
+
+1;
+
+
diff --git a/modules/Bio/EnsEMBL/SplicingEvent.pm b/modules/Bio/EnsEMBL/SplicingEvent.pm
new file mode 100644
index 0000000000000000000000000000000000000000..66ddff439a0c58653ab0c69c5c287c8577e0eae5
--- /dev/null
+++ b/modules/Bio/EnsEMBL/SplicingEvent.pm
@@ -0,0 +1,149 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::SlicingEvent - Object representing an alternative splicing event
+
+=head1 SYNOPSIS
+
+ my $ase = Bio::EnsEMBL::SplicingEvent->new(
+ -START => 123,
+ -END => 1045,
+ -STRAND => 1,
+ -GENE_ID => $gene->dbID,
+ -SLICE => $slice
+ );
+
+ # set some additional attributes
+ $ase->name('ENSG00000000003-CNE-3');
+ $ase->type('CNE');
+
+=head1 DESCRIPTION
+
+A representation of an Alternative Splicing Event within the Ensembl system.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SplicingEvent;
+
+use strict;
+
+use POSIX;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+
+## Add to gene get_all_splicing_events
+
+
+
+sub gene_id{
+ my $self = shift;
+ $self->{'gene_id'} = shift if (@_);
+
+ if (defined $self->{'gene_id'}) {
+ return $self->{'gene_id'};
+ }
+
+ return undef;
+}
+
+sub name{
+ my $self = shift;
+ $self->{'name'} = shift if (@_);
+
+ if (defined $self->{'name'}) {
+ return $self->{'name'};
+ }
+
+ return undef;
+}
+
+sub type{
+ my $self = shift;
+ $self->{'type'} = shift if (@_);
+
+ if (defined $self->{'type'}) {
+ return $self->{'type'};
+ }
+
+ return undef;
+}
+
+sub add_Feature{
+ my ($self, $feat) = @_;
+
+ if( !ref $feat || ! $feat->isa("Bio::EnsEMBL::SplicingEventFeature") ) {
+ throw("$feat is not a Bio::EnsEMBL::SplicingEventFeature!");
+ }
+
+ $self->{'_feature_array'} ||= [];
+ push(@{$self->{'_feature_array'}},$feat);
+}
+
+
+sub get_all_Features {
+ my $self = shift;
+
+ if( ! exists $self->{'_feature_array'} ) {
+ if( defined $self->adaptor() ) {
+ my $fta = $self->adaptor()->db()->get_SplicingEventFeatureAdaptor();
+ my $features = $fta->fetch_all_by_SplicingEvent( $self );
+ $self->{'_feature_array'} = $features;
+ }
+ }
+ return $self->{'_feature_array'};
+}
+
+sub add_Pair{
+ my ($self, $feat) = @_;
+
+ if( !ref $feat || ! $feat->isa("Bio::EnsEMBL::SplicingEventPair") ) {
+ throw("$feat is not a Bio::EnsEMBL::SplicingEventPair!");
+ }
+
+ $self->{'_pair_array'} ||= [];
+ push(@{$self->{'_pair_array'}},$feat);
+}
+
+
+sub get_all_Pairs {
+ my $self = shift;
+
+ if( ! exists $self->{'_pair_array'} ) {
+ if( defined $self->adaptor() ) {
+ my $pa = $self->adaptor()->db()->get_SplicingTranscriptPairAdaptor();
+ my $pairs = $pa->fetch_all_by_SplicingEvent( $self );
+ $self->{'_pair_array'} = $pairs;
+ }
+ }
+ return $self->{'_pair_array'};
+}
+
+
+1;
diff --git a/modules/Bio/EnsEMBL/SplicingEventFeature.pm b/modules/Bio/EnsEMBL/SplicingEventFeature.pm
new file mode 100644
index 0000000000000000000000000000000000000000..064f39fd0b1e498af462547d7021f3870e2ab666
--- /dev/null
+++ b/modules/Bio/EnsEMBL/SplicingEventFeature.pm
@@ -0,0 +1,143 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::SplicingEventFeature - Object representing an alternative splicing event
+
+=head1 SYNOPSIS
+
+ my $ase = Bio::EnsEMBL::SplicingEventFeature->new(
+ -START => 123,
+ -END => 1045,
+ -EXON_ID => $exon->dbID
+ );
+
+ # set some additional attributes
+ $ase->type('flanking_exon');
+
+=head1 DESCRIPTION
+
+A representation of an Alternative Splicing Event Feature within the Ensembl system.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SplicingEventFeature;
+
+use strict;
+
+use POSIX;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+
+## Add to gene get_all_splicing_events
+
+
+
+sub exon_id{
+ my $self = shift;
+ $self->{'exon_id'} = shift if (@_);
+
+ if (defined $self->{'exon_id'}) {
+ return $self->{'exon_id'};
+ }
+
+ return undef;
+}
+
+sub transcript_id{
+ my $self = shift;
+ $self->{'transcript_id'} = shift if (@_);
+
+ if (defined $self->{'transcript_id'}) {
+ return $self->{'transcript_id'};
+ }
+
+ return undef;
+}
+
+sub feature_order{
+ my $self = shift;
+ $self->{'feature_order'} = shift if (@_);
+
+ if (defined $self->{'feature_order'}) {
+ return $self->{'feature_order'};
+ }
+
+ return undef;
+}
+
+sub type{
+ my $self = shift;
+ $self->{'type'} = shift if (@_);
+
+ if (defined $self->{'type'}) {
+ return $self->{'type'};
+ }
+
+ return undef;
+}
+
+sub start{
+ my $self = shift;
+ $self->{'start'} = shift if (@_);
+
+ if (defined $self->{'start'}) {
+ return $self->{'start'};
+ }
+
+ return undef;
+}
+
+sub end{
+ my $self = shift;
+ $self->{'end'} = shift if (@_);
+
+ if (defined $self->{'end'}) {
+ return $self->{'end'};
+ }
+
+ return undef;
+}
+
+
+sub transcript_association{
+ my $self = shift;
+ $self->{'transcript_association'} = shift if (@_);
+
+ if (defined $self->{'transcript_association'}) {
+ return $self->{'transcript_association'};
+ }
+
+ return undef;
+}
+
+
+
+
+1;
diff --git a/modules/Bio/EnsEMBL/SplicingTranscriptPair.pm b/modules/Bio/EnsEMBL/SplicingTranscriptPair.pm
new file mode 100644
index 0000000000000000000000000000000000000000..957908aefd3d14d78029f647c56d52495e4eae53
--- /dev/null
+++ b/modules/Bio/EnsEMBL/SplicingTranscriptPair.pm
@@ -0,0 +1,106 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2009 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::SplicingTranscriptPair - Object representing an alternative splicing transcript pair
+
+=head1 SYNOPSIS
+
+ my $ase = Bio::EnsEMBL::SplicingTranscriptPair->new(
+ -START => 123,
+ -END => 1045,
+ -TRANSCRIPT_ID_1 => $tran1->dbID,
+ -TRANSCRIPT_ID_2 => %tran2->dbID
+ );
+
+=head1 DESCRIPTION
+
+A representation of an Alternative Splicing Transcrript Pair within the Ensembl system.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SplicingTranscriptPair;
+
+use strict;
+
+use POSIX;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+
+
+sub transcript_id_1{
+ my $self = shift;
+ $self->{'transcript_id_1'} = shift if (@_);
+
+ if (defined $self->{'transcript_id_1'}) {
+ return $self->{'transcript_id_1'};
+ }
+
+ return undef;
+}
+
+sub transcript_id_2{
+ my $self = shift;
+ $self->{'transcript_id_2'} = shift if (@_);
+
+ if (defined $self->{'transcript_id_2'}) {
+ return $self->{'transcript_id_2'};
+ }
+
+ return undef;
+}
+
+
+sub start{
+ my $self = shift;
+ $self->{'start'} = shift if (@_);
+
+ if (defined $self->{'start'}) {
+ return $self->{'start'};
+ }
+
+ return undef;
+}
+
+sub end{
+ my $self = shift;
+ $self->{'end'} = shift if (@_);
+
+ if (defined $self->{'end'}) {
+ return $self->{'end'};
+ }
+
+ return undef;
+}
+
+
+
+
+
+1;