First attempt retrieving splicing event data from the core database

modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm

+=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;
+
+

modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm

+=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;
+
+

modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm

+=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;
+
+

modules/Bio/EnsEMBL/SplicingEvent.pm

+=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;

modules/Bio/EnsEMBL/SplicingEventFeature.pm

+=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;

modules/Bio/EnsEMBL/SplicingTranscriptPair.pm

+=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;