diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm index 67551754041d6b8ceecc97892ed4d0eeec18ae9b..fde650c15ec21244e9136df0ec87a2ed1940d578 100644 --- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm +++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm @@ -141,7 +141,8 @@ sub fetch_by_stable_id_version { SELECT m.new_db_name, m.new_release, - m.new_assembly + m.new_assembly, + sie.score FROM stable_id_event sie, mapping_session m WHERE sie.mapping_session_id = m.mapping_session_id AND sie.new_stable_id = "$stable_id" @@ -153,7 +154,7 @@ sub fetch_by_stable_id_version { my $sth = $self->prepare($sql); $sth->execute(); - my ($db_name, $release, $assembly) = $sth->fetchrow_array(); + my ($db_name, $release, $assembly, $score) = $sth->fetchrow_array(); $sth->finish(); # you might have missed a stable ID that was deleted in the very first @@ -163,7 +164,8 @@ sub fetch_by_stable_id_version { SELECT m.old_db_name, m.old_release, - m.old_assembly + m.old_assembly, + sie.score FROM stable_id_event sie, mapping_session m WHERE sie.mapping_session_id = m.mapping_session_id AND sie.old_stable_id = "$stable_id" @@ -175,7 +177,7 @@ sub fetch_by_stable_id_version { $sth = $self->prepare($sql); $sth->execute(); - ($db_name, $release, $assembly) = $sth->fetchrow_array(); + ($db_name, $release, $assembly, $score) = $sth->fetchrow_array(); $sth->finish(); } @@ -186,6 +188,7 @@ sub fetch_by_stable_id_version { $arch_id->db_name($db_name); $arch_id->release($release); $arch_id->assembly($assembly); + $arch_id->score($score); } return $arch_id; @@ -325,6 +328,7 @@ sub fetch_predecessors_by_archive_id { SELECT sie.old_stable_id, sie.old_version, + sie.score, m.old_db_name, m.old_release, m.old_assembly @@ -339,8 +343,8 @@ sub fetch_predecessors_by_archive_id { $sth->bind_param(2, $arch_id->db_name, SQL_VARCHAR); $sth->execute(); - my ($old_stable_id, $old_version, $old_db_name, $old_release, $old_assembly); - $sth->bind_columns(\$old_stable_id, \$old_version, \$old_db_name, \$old_release, \$old_assembly); + my ($old_stable_id, $old_version, $score, $old_db_name, $old_release, $old_assembly); + $sth->bind_columns(\$old_stable_id, \$old_version, \$score, \$old_db_name, \$old_release, \$old_assembly); while( $sth->fetch() ) { if( defined $old_stable_id ) { @@ -351,7 +355,8 @@ sub fetch_predecessors_by_archive_id { -db_name => $old_db_name, -release => $old_release, -assembly => $old_assembly, - -adaptor => $self + -adaptor => $self, + -score => $score ); _resolve_type( $old_arch_id ); push( @result, $old_arch_id ); @@ -373,6 +378,7 @@ sub fetch_predecessors_by_archive_id { SELECT sie.new_stable_id, sie.new_version, + sie.score, m.new_db_name, m.new_release, m.new_assembly @@ -387,7 +393,7 @@ sub fetch_predecessors_by_archive_id { $sth->bind_param(2,$prev_dbname, SQL_VARCHAR); $sth->execute(); - $sth->bind_columns(\$old_stable_id, \$old_version, \$old_db_name, \$old_release, \$old_assembly); + $sth->bind_columns(\$old_stable_id, \$old_version, \$score, \$old_db_name, \$old_release, \$old_assembly); while( $sth->fetch() ) { if (defined $old_stable_id) { @@ -398,7 +404,8 @@ sub fetch_predecessors_by_archive_id { -db_name => $old_db_name, -release => $old_release, -assembly => $old_assembly, - -adaptor => $self + -adaptor => $self, + -score => $score ); _resolve_type( $old_arch_id ); push( @result, $old_arch_id ); @@ -444,6 +451,7 @@ sub fetch_successors_by_archive_id { SELECT sie.new_stable_id, sie.new_version, + sie.score, m.new_db_name, m.new_release, m.new_assembly @@ -458,8 +466,8 @@ sub fetch_successors_by_archive_id { $sth->bind_param(2,$arch_id->db_name,SQL_VARCHAR); $sth->execute(); - my ($new_stable_id, $new_version, $new_db_name, $new_release, $new_assembly); - $sth->bind_columns(\$new_stable_id, \$new_version, \$new_db_name, \$new_release, \$new_assembly); + my ($new_stable_id, $new_version, $score, $new_db_name, $new_release, $new_assembly); + $sth->bind_columns(\$new_stable_id, \$new_version, \$score, \$new_db_name, \$new_release, \$new_assembly); while( $sth->fetch() ) { if( defined $new_stable_id ) { @@ -470,7 +478,8 @@ sub fetch_successors_by_archive_id { -db_name => $new_db_name, -release => $new_release, -assembly => $new_assembly, - -adaptor => $self + -adaptor => $self, + -score => $score ); _resolve_type($new_arch_id); @@ -493,6 +502,7 @@ sub fetch_successors_by_archive_id { SELECT sie.old_stable_id, sie.old_version, + sie.score, m.old_db_name, m.old_release, m.old_assembly @@ -507,7 +517,7 @@ sub fetch_successors_by_archive_id { $sth->bind_param(2, $next_dbname, SQL_VARCHAR); $sth->execute(); - $sth->bind_columns(\$new_stable_id, \$new_version, \$new_db_name, \$new_release, \$new_assembly); + $sth->bind_columns(\$new_stable_id, \$new_version, \$score, \$new_db_name, \$new_release, \$new_assembly); while( $sth->fetch() ) { if (defined $new_stable_id) { @@ -518,7 +528,8 @@ sub fetch_successors_by_archive_id { -db_name => $new_db_name, -release => $new_release, -assembly => $new_assembly, - -adaptor => $self + -adaptor => $self, + -score => $score ); _resolve_type($new_arch_id); @@ -888,7 +899,8 @@ sub _lookup_version { m.new_db_name, m.new_release, m.new_assembly, - sie.new_version + sie.new_version, + sie.score FROM stable_id_event sie, mapping_session m WHERE sie.mapping_session_id = m.mapping_session_id AND new_stable_id = "@{[$arch_id->stable_id]}" @@ -903,7 +915,8 @@ sub _lookup_version { m.old_db_name, m.old_release, m.old_assembly, - sie.old_version + sie.old_version, + sie.score FROM stable_id_event sie, mapping_session m WHERE sie.mapping_session_id = m.mapping_session_id AND sie.old_stable_id = "@{[$arch_id->stable_id]}" @@ -914,7 +927,7 @@ sub _lookup_version { my $sth = $self->prepare($sql); $sth->execute(); - my ($db_name, $release, $assembly, $version) = $sth->fetchrow_array(); + my ($db_name, $release, $assembly, $version, $score) = $sth->fetchrow_array(); $sth->finish(); # you might have missed a stable ID that was deleted in the very first @@ -925,7 +938,8 @@ sub _lookup_version { m.old_db_name, m.old_release, m.old_assembly, - sie.old_version + sie.old_version, + sie.score FROM stable_id_event sie, mapping_session m WHERE sie.mapping_session_id = m.mapping_session_id AND old_stable_id = "@{[$arch_id->stable_id]}" @@ -937,7 +951,7 @@ sub _lookup_version { $sth = $self->prepare($sql); $sth->execute(); - ($db_name, $release, $assembly, $version) = $sth->fetchrow_array(); + ($db_name, $release, $assembly, $version, $score) = $sth->fetchrow_array(); $sth->finish(); } @@ -950,6 +964,7 @@ sub _lookup_version { $arch_id->db_name($db_name); $arch_id->release($release); $arch_id->assembly($assembly); + $arch_id->score($score); } }