diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm
new file mode 100644
index 0000000000000000000000000000000000000000..90db4302141625d1e3d169e6941edc95510e4db4
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm
@@ -0,0 +1,349 @@
+# EnsEMBL module for DitagAdaptor
+#
+# Copyright EMBL-EBI/Wellcome Trust Sanger Center 2006
+#
+# You may distribute this module under the same terms as perl itself
+#
+# Cared for by EnsEMBL (ensembl-dev@ebi.ac.uk)
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Map::DBSQL::DitagAdaptor
+
+=head1 SYNOPSIS
+
+my $ditagadaptor = $db->get_DitagAdaptor();
+my @ditags = @{ $ditagadaptor->fetch_by_type("ZZ11") };
+
+=head1 DESCRIPTION
+
+Provides database interaction for the Bio::EnsEMBL::Map::Ditag object
+
+=cut
+
+package Bio::EnsEMBL::Map::DBSQL::DitagAdaptor;
+
+use strict;
+use vars ('@ISA');
+
+use Bio::EnsEMBL::Map::Ditag;
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+
+=head2 fetch_by_name
+
+ Arg [1] : ditag name
+ Example : $tag = $ditag_adaptor->fetch_by_name("U3");
+ Description: Retrieves ditags from the database using the name
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : general
+
+=cut
+
+sub fetch_by_name {
+ my ($self, $tagname) = @_;
+
+ if(!$tagname){
+ throw "must be called with a name of a ditag.";
+ }
+ my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
+ FROM ditag d
+ WHERE d.name = ?");
+ $sth->execute($tagname);
+ my $result = $self->_fetch($sth);
+
+ return $result;
+
+}
+
+
+=head2 fetch_by_dbID
+
+ Arg [1] : ditag type
+ Example : @all_tags = @{$ditag_adaptor->fetch_by_dbID(1003)};
+ Description: Retrieve ditags with a certain id from the database
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : general
+
+=cut
+
+sub fetch_by_dbID {
+ my ($self, $tagid) = @_;
+
+ if(!$tagid){
+ throw "must be called with the type of a ditag.";
+ }
+ my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
+ FROM ditag d
+ WHERE d.ditag_id = ?");
+ $sth->execute($tagid);
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_all_by_type
+
+ Arg [1] : ditag type
+ Example : @all_tags = @{$ditag_adaptor->fetch_by_type("SME005")};
+ Description: Retrieves all ditags of a certain type from the database
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : general
+
+=cut
+
+sub fetch_all_by_type {
+ my ($self, $tagtype) = @_;
+
+ if(!$tagtype){
+ throw "must be called with the type of a ditag.";
+ }
+ my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
+ FROM ditag d
+ WHERE d.type = ?");
+ $sth->execute($tagtype);
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_all_by_name_and_type
+
+ Arg [1] : ditag name
+ Arg [2] : ditag type
+ Example : $tag = $ditag_adaptor->fetch_by_name_and_type("U3", "SME005");
+ Description: Retrieves ditags from the database using name/type combination
+ which should be non-ambiguous
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : general
+
+=cut
+
+sub fetch_all_by_name_and_type {
+ my ($self, $tagname, $tagtype) = @_;
+
+ if(!$tagname or !$tagtype){
+ throw "must be called with a name and type of a ditag.";
+ }
+ my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
+ FROM ditag d
+ WHERE d.name = ? and d.type = ?");
+ $sth->execute($tagname, $tagtype);
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_all
+
+ Args : none
+ Example : @all_tags = @{$ditag_adaptor->fetch_all};
+ Description: Retrieves all ditags from the database
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : general
+
+=cut
+
+sub fetch_all {
+ my ($self) = @_;
+
+ my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
+ FROM ditag d");
+ $sth->execute;
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_with_limit
+
+ Arg [1] : ditag type
+ Arg [2] : row limit
+ Arg [3] : row offset
+ Description: fetch_by_type with row limit and offset
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+
+=cut
+
+sub fetch_with_limit {
+ my ($self, $tagtype, $limit, $offset) = @_;
+
+ my @ditags = ();
+ print STDERR "> $tagtype, $limit, $offset\n";
+ my $sql = "SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence ".
+ "FROM ditag d ".
+ "WHERE d.type = ? LIMIT ? OFFSET ?;";
+ my $sth = $self->db->dbc->prepare($sql);
+ $sth->execute($tagtype, $limit, $offset);
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 _fetch
+
+ Arg [1] : statement handler object
+ Description: generic sql-fetch function for the ditag fetch methods
+ Returntype : listref of Bio::EnsEMBL::Map::Ditag
+ Caller : private
+
+=cut
+
+sub _fetch {
+ my ($self, $sth) = @_;
+
+ my($tag_id, $name, $type, $count, $sequence);
+ my @tags;
+
+ $sth->bind_columns(\$tag_id, \$name, \$type, \$count, \$sequence);
+ while($sth->fetch) {
+ push @tags, Bio::EnsEMBL::Map::Ditag->new (
+ -dbID => $tag_id,
+ -name => $name,
+ -type => $type,
+ -tag_count => $count,
+ -sequence => $sequence,
+ -adaptor => $self,
+ );
+ }
+
+ return \@tags;
+}
+
+
+=head2 store
+
+ Arg [1] : Bio::EnsEMBL::Map::Ditag
+ Example : $ditag_adaptor->store(\@ditags);
+ Description: Stores a single ditag or
+ a list of ditags in this database.
+ Returntype : none
+ Caller : general
+
+=cut
+
+sub store {
+ my ($self, $ditags) = @_;
+
+ if(ref $ditags eq 'ARRAY'){
+ if(scalar(@$ditags) == 0){
+ throw("Must call store with ditag or list ref of ditags");
+ }
+ }
+ elsif($ditags){
+ my @ditags;
+ push @ditags, $ditags;
+ $ditags = \@ditags;
+ }
+ else{
+ throw("Must call store with ditag or list ref of ditags not ".$ditags);
+ }
+
+ my $db = $self->db() or throw "Couldn t get database connection.";
+
+ TAG:
+ foreach my $ditag (@$ditags) {
+
+ if ( !ref $ditag || !$ditag->isa("Bio::EnsEMBL::Map::Ditag") ) {
+ throw( "Object must be an Ensembl Ditag, " . "not a [" . ref($ditag) . "]" );
+ }
+
+# if ( $ditag->is_stored($db) ) {
+# warning( "Ditag [" . $ditag->dbID . "] is already stored in this database." );
+# next TAG;
+# }
+
+ #check if tag with same name/type exists
+ my $sth = $self->prepare( "SELECT COUNT(*) FROM ditag
+ WHERE name = ? AND type = ?" );
+ $sth->execute($ditag->name, $ditag->type);
+ if($sth->fetchrow() > 0){
+ warning( "Ditag with name/type ".$ditag->name." / ".$ditag->type.
+ " is already stored in this database." );
+ next TAG;
+ }
+
+ if ( $ditag->dbID ) {
+ my $sth = $self->prepare( "INSERT INTO ditag( ditag_id , name, type, tag_count, sequence ) ".
+ "VALUES( ?,?,?,?,? )" );
+ $sth->bind_param(1,$ditag->dbID,SQL_INTEGER);
+ $sth->bind_param(2,$ditag->name,SQL_VARCHAR);
+ $sth->bind_param(3,$ditag->type,SQL_VARCHAR);
+ $sth->bind_param(4,$ditag->tag_count,SQL_VARCHAR);
+ $sth->bind_param(5,$ditag->sequence,SQL_VARCHAR);
+ $sth->execute();
+ } else {
+ my $sth = $self->prepare( "INSERT INTO ditag( name, type, tag_count, sequence ) ".
+ "VALUES( ?,?,?,? )" );
+ $sth->bind_param(1,$ditag->name,SQL_VARCHAR);
+ $sth->bind_param(2,$ditag->type,SQL_VARCHAR);
+ $sth->bind_param(3,$ditag->tag_count,SQL_VARCHAR);
+ $sth->bind_param(4,$ditag->sequence,SQL_VARCHAR);
+ $sth->execute();
+ my $dbID = $sth->{'mysql_insertid'};
+ $ditag->dbID($dbID);
+ $ditag->adaptor($self);
+ }
+ }
+
+ return 1;
+}
+
+
+=head2 print_creation
+
+ Arg [1] : ditag probe name
+ Arg [2] : ditag type
+ Arg [3] : ditag count
+ Arg [4] : ditag sequence
+ Arg [5] : (optional) ditag dbID
+ Description: convenience method to produce SQL insert statements
+ to speed up the creation of new ditags
+ Returntype : string
+
+=cut
+
+sub print_creation {
+ my ($self, $probe_name, $type, $count, $sequence, $dbid) = @_;
+ my $string;
+ if($dbid){
+ $string = "INSERT INTO ditag( ditag_id, name, type, tag_count, sequence ) ".
+ "VALUES($dbid, '".$probe_name."', '".$type."', ".$count."'".$sequence."');\n";
+ }
+ else {
+ $string = "INSERT INTO ditag( name, type, tag_count, sequence ) ".
+ "VALUES('".$probe_name."', '".$type."', ".$count.", '".$sequence."');\n";
+ }
+
+ return $string;
+}
+
+
+=head2 list_dbIDs
+
+ Args : None
+ Example : my @feature_ids = @{$da->list_dbIDs()};
+ Description: Gets an array of internal IDs for all Ditag objects in
+ the current database.
+ Returntype : List of ints
+ Exceptions : None
+
+=cut
+
+sub list_dbIDs {
+ my $self = shift;
+
+ return $self->_list_dbIDs('ditag');
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
new file mode 100644
index 0000000000000000000000000000000000000000..c0034743f97130bc9a45dc008fbe23bfa7d43a45
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
@@ -0,0 +1,579 @@
+# EnsEMBL module for DitagFeatureAdaptor
+#
+# Copyright EMBL-EBI/Wellcome Trust Sanger Center 2006
+#
+# You may distribute this module under the same terms as perl itself
+#
+# Cared for by EnsEMBL (ensembl-dev@ebi.ac.uk)
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor
+
+=head1 SYNOPSIS
+
+my $dfa = $db->get_DitagFeatureAdaptor;
+my $ditagFeatures = $dfa->fetch_by_ditag_id(123);
+foreach my $ditagFeature (@$ditagFeatures){
+ print $ditagFeature->ditag_id . " " .
+ $ditagFeature->slice . " " . $ditagFeature->start . "-" .
+ $ditagFeature->end . " " . $ditagFeature->strand;
+}
+
+=head1 DESCRIPTION
+
+Provides database interaction for the Bio::EnsEMBL::Map::DitagFeature object
+
+=cut
+
+package Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor;
+
+use strict;
+use vars ('@ISA');
+
+use Bio::EnsEMBL::Map::Ditag;
+use Bio::EnsEMBL::Map::DitagFeature;
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+
+=head2 fetch_all
+
+ Arg [1] : none
+ Example : @all_tags = @{$ditagfeature_adaptor->fetch_all};
+ Description: Retrieves all ditagFeatures from the database
+ Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
+ Caller : general
+
+=cut
+
+sub fetch_all {
+ my $self = shift;
+
+ my $sth = $self->prepare("SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
+ hit_strand, cigar_line, ditag_side, ditag_pair_id
+ FROM ditag_feature" );
+ $sth->execute;
+
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_by_dbID
+
+ Arg [1] : ditagFeature dbID
+ Example : @my_tags = @{$ditagfeature_adaptor->fetch_by_dbID($my_id)};
+ Description: Retrieves a ditagFeature from the database.
+ Returntype : Bio::EnsEMBL::Map::DitagFeature
+ Caller : general
+
+=cut
+
+sub fetch_by_dbID {
+ my ($self, $dbid) = @_;
+
+ my $sth = $self->prepare("SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
+ hit_strand, cigar_line, ditag_side, ditag_pair_id
+ FROM ditag_feature
+ WHERE ditag_feature_id = ?" );
+ $sth->execute($dbid);
+
+ my $result = $self->_fetch($sth);
+
+ return $result->[0];
+}
+
+
+=head2 fetch_by_ditagID
+
+ Arg [1] : ditag dbID
+ Example : @my_tags = @{$ditagfeature_adaptor->fetch_by_ditag_id($my_id)};
+ Description: Retrieves all ditagFeatures from the database linking to a specific ditag-id
+ Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
+ Caller : general
+
+=cut
+
+sub fetch_by_ditagID {
+ my ($self, $ditag_id) = @_;
+
+print "\nID=$ditag_id\n";
+
+ my $sth = $self->prepare("SELECT ditag_feature_id, ditag_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
+ hit_strand, cigar_line, ditag_side, ditag_pair_id
+ FROM ditag_feature
+ WHERE ditag_id = ?
+ ORDER BY ditag_pair_id" );
+ $sth->execute($ditag_id);
+
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_all_by_type
+
+ Arg [1] : ditag type
+ Example : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_type($type)};
+ Description: Retrieves all ditagFeatures from the database linking to a specific ditag-type
+ Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
+ Caller : general
+
+=cut
+
+sub fetch_all_by_type {
+ my ($self, $ditag_type) = @_;
+
+ my $sth = $self->prepare("SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
+ df.seq_region_start, df.seq_region_end, df.seq_region_strand,
+ df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
+ df.cigar_line, df.ditag_side, ditag_pair_id
+ FROM ditag_feature df, ditag d
+ WHERE df.ditag_id=d.ditag_id and d.type = ?
+ ORDER BY df.ditag_id, df.ditag_pair_id" );
+ $sth->execute($ditag_type);
+
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+
+=head2 fetch_all_by_Slice
+
+ Arg [1] : Bio::EnsEMBL::Slice
+ Arg [2] : (optional) ditag type
+ Example : $tag = $ditagfeature_adaptor->fetch_all_by_Slice($slice, "SME005");
+ Description: Retrieves ditagFeatures from the database for a specific region
+ and (optional) ditag type.
+ Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
+ Caller : general
+
+=cut
+
+sub fetch_all_by_Slice {
+ my ($self, $slice, $tagtype) = @_;
+
+ if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
+ throw("Bio::EnsEMBL::Slice argument expected.");
+ }
+
+ my $sql = "SELECT df.ditag_feature_id, df.ditag_id, df.seq_region_id,
+ df.seq_region_start, df.seq_region_end, df.seq_region_strand,
+ df.analysis_id, df.hit_start, df.hit_end, df.hit_strand,
+ df.cigar_line, df.ditag_side, ditag_pair_id
+ FROM ditag_feature df, ditag d
+ WHERE df.ditag_id=d.ditag_id AND df.seq_region_id = ?
+ AND df.seq_region_start >= ? AND df.seq_region_end <= ? ";
+ if($tagtype){
+ $sql .= " and d.type = ? ";
+ }
+ $sql .= "ORDER BY ditag_pair_id";
+ my $sth = $self->prepare($sql);
+ if($tagtype){
+ $sth->execute($slice->get_seq_region_id, $slice->start, $slice->end, $tagtype);
+ }
+ else{
+ $sth->execute($slice->get_seq_region_id, $slice->start, $slice->end);
+ }
+ my $result = $self->_fetch($sth);
+
+ return $result;
+}
+
+
+=head2 fetch_grouped
+
+ Arg [1] : (optional) ditag id
+ Arg [2] : (optional) ditag type
+ Arg [3] : (optional) Bio::EnsEMBL::Slice
+ Example : $gouped_tags = $ditagfeature_adaptor->fetch_grouped(undef, "ZZ11", undef);
+ Description: Retrieves Features from the database in their start-end groups;
+ The start will be the lower seq_region_start, the end the higher seq_region_end.
+ In context this should refer to potential transcript start and end locations.
+ Returntype : listref of hashes similar to DitagFeatures:
+ %grouped_tag( -slice => $slice,
+ -start => $seqstart,
+ -end => $seqend,
+ -strand => $strand,
+ -tag_count => $tagcount,
+ -hit_strand => $hit_strand,
+ -ditag_id => $ditag_id,
+ -ditag_pair_id => $ditag_pair_id,
+ );
+ Caller : general
+
+=cut
+
+sub fetch_grouped {
+ my ($self, $ditagid, $tagtype, $slice) = @_;
+
+ my (@grouped_tags, @querywords);
+ my $sql = "SELECT df.seq_region_id, MIN(df.seq_region_start) AS minstart,
+ MAX(df.seq_region_end) AS maxend, df.seq_region_strand,
+ df.hit_strand, df.ditag_id, df.ditag_pair_id, d.tag_count
+ FROM ditag_feature df, ditag d
+ WHERE df.ditag_id=d.ditag_id ";
+
+ if($tagtype){
+ $sql .= " AND d.type = \"".$tagtype."\"";
+ }
+ if($ditagid){
+ $sql .= " AND df.ditag_id = ".$ditagid;
+ }
+ if($slice){
+ $sql .= " AND df.seq_region_id = ".$slice->get_seq_region_id.
+ " AND df.seq_region_start >= ".$slice->start.
+ " AND df.seq_region_end <= ".$slice->end;
+ }
+ $sql .= " GROUP BY df.ditag_id, df.ditag_pair_id".
+ " ORDER BY df.seq_region_id, minstart, maxend";
+
+ my $sth = $self->prepare($sql);
+ $sth->execute();
+
+ my ( $seqreg, $seqstart, $seqend, $strand, $hit_strand, $ditag_id, $ditag_pair_id, $tagcount );
+ $sth->bind_columns( \$seqreg, \$seqstart, \$seqend,
+ \$strand, \$hit_strand, \$ditag_id,
+ \$ditag_pair_id, \$tagcount );
+
+ while ( $sth->fetch ) {
+ my $alt_slice = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);
+
+ my %grouped_tag = ( slice => $alt_slice,
+ start => $seqstart,
+ end => $seqend,
+ strand => $strand,
+ tag_count => $tagcount,
+ hit_strand => $hit_strand,
+ ditag_id => $ditag_id,
+ ditag_pair_id => $ditag_pair_id,
+ );
+ push @grouped_tags, \%grouped_tag;
+ }
+
+ return \@grouped_tags;
+}
+
+
+=head2 _fetch
+
+ Arg [1] : statement handler
+ Description: generic sql-fetch function for the DitagFeature fetch methods
+ Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
+ Caller : private
+
+=cut
+
+sub _fetch {
+ my ($self, $sth) = @_;
+
+ my ( $tag_id, $mothertag_id, $seqreg, $seqstart, $seqend, $strand, $analysis_id, $hit_start,
+ $hit_end, $hit_strand, $cigar_line, $ditag_side, $ditag_pair_id );
+ $sth->bind_columns( \$tag_id, \$mothertag_id, \$seqreg,
+ \$seqstart, \$seqend, \$strand,
+ \$analysis_id, \$hit_start, \$hit_end,
+ \$hit_strand, \$cigar_line, \$ditag_side,
+ \$ditag_pair_id );
+
+ my @ditags;
+
+ while ( $sth->fetch ) {
+ my $analysis_obj = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
+ my $slice = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);
+
+ push @ditags,
+ Bio::EnsEMBL::Map::DitagFeature->new( -dbid => $tag_id,
+ -slice => $slice,
+ -start => $seqstart,
+ -end => $seqend,
+ -strand => $strand,
+ -analysis => $analysis_obj,
+ -hit_start => $hit_start,
+ -hit_end => $hit_end,
+ -hit_strand => $hit_strand,
+ -ditag_id => $mothertag_id,
+ -cigar_line => $cigar_line,
+ -ditag_side => $ditag_side,
+ -ditag_pair_id => $ditag_pair_id,
+ -adaptor => $self,
+ );
+ }
+
+ return \@ditags;
+}
+
+
+=head2 sequence
+
+ Arg [1] : dbID of DitagFeature
+ Example : $ditagfeature_adaptor->get_sequence($ditagFeature->dbID)
+ Description: get the part of the sequence of a ditag,
+ that is actully aligned to the genome.
+ Returntype : string
+ Exceptions : thrown if not all data needed for storing is populated in the
+ ditag features
+ Caller : Bio::EnsEMBL::Map::DitagFeature
+
+=cut
+
+sub sequence {
+ my ($self, $dbID) = @_;
+
+ my $sequence = undef;
+ my $db = $self->db() or throw "Couldn t get database connection.";
+ my $sql = "SELECT d.sequence, df.hit_start, df.hit_end, df.hit_strand ".
+ "FROM ditag d, ditag_feature df ".
+ "WHERE df.ditag_id=d.ditag_id and df.ditag_feature_id = ?";
+ my $sth = $db->dbc->prepare($sql);
+ $sth->execute( $dbID );
+ my ($seq, $start, $end, $strand) = $sth->fetchrow_array();
+ if($seq and $start and $end and $strand){
+ $sequence = substr($seq, ($start-1), ($end-$strand));
+ if($strand == -1) {
+ $sequence =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;
+ }
+ }
+
+ return $sequence;
+}
+
+
+=head2 store
+
+ Arg [1] : (Array ref of) Bio::EnsEMBL::Map::DitagFeature
+ Example : $ditagfeature_adaptor->store(@ditag_features);
+ Description: Stores a single ditagFeature or
+ a list of ditagFeatures in this database.
+ Returntype : none
+ Exceptions : thrown if not all data needed for storing is populated in the
+ ditag features
+ Caller : general
+
+=cut
+
+sub store {
+ my ( $self, $ditags ) = @_;
+
+ if ( ref $ditags eq 'ARRAY' ) {
+ if ( scalar(@$ditags) == 0 ) {
+ throw( "Must call store with ditagFeature or list ref of ditagsFeature" );
+ }
+ } elsif ($ditags) {
+ my @ditags;
+ push @ditags, $ditags;
+ $ditags = \@ditags;
+ } else {
+ throw( "Must call store with ditagFeature or list ref of ditagsFeature." );
+ }
+
+ my $db = $self->db() or throw "Couldn t get database connection.";
+
+ my $sth1 = $self->prepare( "INSERT INTO ditag_feature( ditag_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end,
+ hit_strand, cigar_line, ditag_side, ditag_pair_id )
+ VALUES( ?,?,?,?,?,?,?,?,?,?,?,? )" );
+ my $sth2 = $self->prepare( "INSERT INTO ditag_feature( ditag_feature_ID, ditag_id, seq_region_id,
+ seq_region_start, seq_region_end, seq_region_strand, analysis_id, hit_start,
+ hit_end, hit_strand, cigar_line, ditag_side, ditag_pair_id )
+ VALUES( ?,?,?,?,?,?,?,?,?,?,?,?,? )" );
+ my $sth3 = $self->prepare( "SELECT COUNT(*) FROM ditag_feature
+ WHERE ditag_id = ?" );
+
+TAG:
+ foreach my $ditag (@$ditags) {
+
+ if ( !ref $ditag || !$ditag->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
+ throw( "Object must be an Ensembl DitagFeature, "
+ . "not a " . ref($ditag) );
+ }
+
+# if ( $ditag->is_stored($db) ) {
+# warning( "DitagFeature " . $ditag->dbID
+# . " is already stored in this database." );
+# #-->update ?!
+# next TAG;
+# }
+
+# #check if more than 1 tag with this ditag id exist
+# $sth3->execute( $ditag->ditag_id );
+# my ($num) = $sth3->fetchrow_array();
+# if ( ($num) and ($num > 1) ) {
+# warning( "There are already at least 2 DitagFeatures relating to Ditag ".
+# $ditag->ditag_id." stored in this database." );
+# if ( $num > 4 ) {
+# warning( "not storing" );
+# next TAG;
+# }
+# }
+
+ if ( $ditag->dbID ) {
+ $sth2->bind_param( 1, $ditag->dbID, SQL_INTEGER );
+ $sth2->bind_param( 2, $ditag->ditag_id, SQL_INTEGER );
+ $sth2->bind_param( 3, ($ditag->slice->get_seq_region_id), SQL_INTEGER );
+ $sth2->bind_param( 4, $ditag->start, SQL_INTEGER );
+ $sth2->bind_param( 5, $ditag->end, SQL_INTEGER );
+ $sth2->bind_param( 6, $ditag->strand, SQL_VARCHAR );
+ $sth2->bind_param( 7, $ditag->analysis->dbID, SQL_INTEGER );
+ $sth2->bind_param( 8, $ditag->hit_start, SQL_INTEGER );
+ $sth2->bind_param( 9, $ditag->hit_end, SQL_INTEGER );
+ $sth2->bind_param( 10, $ditag->hit_strand, SQL_VARCHAR );
+ $sth2->bind_param( 11, $ditag->cigar_line, SQL_VARCHAR );
+ $sth2->bind_param( 12, $ditag->ditag_side, SQL_VARCHAR );
+ $sth2->bind_param( 13, $ditag->ditag_pair_id, SQL_VARCHAR );
+ $sth2->execute();
+ }
+ else{
+ $sth1->bind_param( 1, $ditag->ditag_id, SQL_INTEGER );
+ $sth1->bind_param( 2, ($ditag->slice->get_seq_region_id), SQL_INTEGER );
+ $sth1->bind_param( 3, $ditag->start, SQL_INTEGER );
+ $sth1->bind_param( 4, $ditag->end, SQL_INTEGER );
+ $sth1->bind_param( 5, $ditag->strand, SQL_VARCHAR );
+ $sth1->bind_param( 6, $ditag->analysis->dbID, SQL_INTEGER );
+ $sth1->bind_param( 7, $ditag->hit_start, SQL_INTEGER );
+ $sth1->bind_param( 8, $ditag->hit_end, SQL_INTEGER );
+ $sth1->bind_param( 9, $ditag->hit_strand, SQL_VARCHAR );
+ $sth1->bind_param( 10, $ditag->cigar_line, SQL_VARCHAR );
+ $sth1->bind_param( 11, $ditag->ditag_side, SQL_VARCHAR );
+ $sth1->bind_param( 12, $ditag->ditag_pair_id, SQL_VARCHAR );
+ $sth1->execute();
+ my $dbID = $sth1->{'mysql_insertid'};
+ $ditag->dbID($dbID);
+ $ditag->adaptor($self);
+ }
+
+ }
+}
+
+
+=head2 batch_store
+
+ Arg [1] : (Array ref of) Bio::EnsEMBL::Map::DitagFeature
+ Example : $ditagfeature_adaptor->batch_store(\@ditag_features);
+ Description: Stores a list of ditagFeatures in this database.
+ DitagFeatures are expected to have no dbID yet.
+ They are inserted in one combined INSERT for better performance.
+ Returntype : none
+ Exceptions : thrown if not all data needed for storing is given for the
+ ditag features
+ Caller : general
+
+=cut
+
+sub batch_store {
+ my ( $self, $ditags ) = @_;
+
+ my %tag_ids = ();
+ my @good_ditags;
+ my ($sql, $sqladd);
+ my $inserts = 0;
+
+ if ( ref $ditags eq 'ARRAY' ) {
+ if ( scalar(@$ditags) == 0 ) {
+ throw( "Must call store with ditagFeature or list ref of ditagsFeature" );
+ }
+ } elsif ($ditags) {
+ my @ditags;
+ push @ditags, $ditags;
+ $ditags = \@ditags;
+ } else {
+ throw( "Must call store with ditagFeature or list ref of ditagsFeature." );
+ }
+
+ my $db = $self->db() or throw "Couldn t get database connection.";
+
+ #check whether it s a DitagFeature object and is not stored already
+ foreach my $ditag (@$ditags) {
+
+ if ( !ref $ditag || !$ditag->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
+ throw( "Object must be an Ensembl DitagFeature, "
+ . "not a " . ref($ditag) );
+ }
+ if ( $ditag->is_stored($db) ) {
+ warning( "DitagFeature " . $ditag->dbID
+ . " is already stored in this database." );
+ next;
+ }
+ $tag_ids{$ditag->ditag_id} = $ditag;
+ push(@good_ditags, $ditag);
+ }
+ $ditags = undef;
+
+# #check if more than 1 tag with this ditag id exists
+# $sql = "SELECT COUNT(*), ditag_id FROM ditag_feature ".
+# "WHERE ditag_id IN (".(join(", ", keys %tag_ids)).") group by ditag_id";
+# my $sth2 = $db->prepare($sql);
+# $sth2->execute();
+# while (my ($num, $ditag_id) = $sth2->fetchrow_array()){
+# if ( ($num) and ($num > 1) ) {
+# warning( "There are already at least 2 DitagFeatures relating to Ditag ".
+# $ditag_id." stored in this database." );
+# if ( $num > 4 ) {
+# warning( "not storing" );
+# next;
+# }
+# }
+# $ditag->ditag_id
+# push(@good_ditags, $tag_ids{$ditag_id});
+# }
+
+ #create batch INSERT
+ $sql = "INSERT INTO ditag_feature ( ditag_id, seq_region_id, seq_region_start, ".
+ "seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
+ "hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
+ foreach my $ditag (@good_ditags) {
+ $sqladd = "";
+ if($inserts){ $sqladd = ", " }
+ $sqladd .= "(". $ditag->ditag_id.", ".($ditag->slice->get_seq_region_id).", ". $ditag->start.", ".
+ $ditag->end.", '".$ditag->strand."', ".$ditag->analysis->dbID.", ".$ditag->hit_start.
+ ", ".$ditag->hit_end.", '".$ditag->hit_strand."', '".$ditag->cigar_line."', '".
+ $ditag->ditag_side."', ".$ditag->ditag_pair_id.")";
+ $sql .= $sqladd;
+ $inserts++;
+ }
+
+ #STORE
+ if($inserts){
+ eval{
+ $db->dbc->do($sql);
+ };
+ if($@){
+ warning("Problem inserting ditag batch!".$@);
+ }
+ }
+ else{
+ warn "Nothing stored!";
+ }
+
+}
+
+
+=head2 list_dbIDs
+
+ Args : None
+ Example : my @feature_ids = @{$dfa->list_dbIDs()};
+ Description: Gets an array of internal IDs for all DitagFeature objects in
+ the current database.
+ Returntype : List of ints
+ Exceptions : None
+
+=cut
+
+sub list_dbIDs {
+ my $self = shift;
+
+ return $self->_list_dbIDs('ditag_feature');
+}
+
+1;