Ported fixes from blanch-ensembl-15-1

modules/Bio/EnsEMBL/External/BlastAdaptor.pm

@@ -10,11 +10,33 @@ use vars qw(@ISA);
 
 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
 use Bio::EnsEMBL::DBSQL::DBConnection;
-#use Bio::Search::HSP::EnsemblHSP; # This is a web module
+use Bio::Search::HSP::EnsemblHSP; # This is a web module
 
 @ISA = qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
 #@ISA = qw( Bio::EnsEMBL::DBSQL::DBConnection );
 
+
+#----------------------------------------------------------------------
+# Define SQL
+
+our $SQL_HSP_STORE = "
+INSERT INTO blast_hsp ( ticket, object, chr_name, chr_start, chr_end )
+VALUES                ( ? , ? , ? , ? , ? )";
+
+our $SQL_HSP_UPDATE = "
+UPDATE  blast_hsp
+SET     object    = ?,
+        chr_name  = ?,
+        chr_start = ?,
+        chr_end   = ?
+WHERE   hsp_id    = ?";
+
+our $SQL_HSP_RETRIEVE = "
+SELECT object
+FROM   blast_hsp
+WHERE  hsp_id = ? ";
+
+
 #----------------------------------------------------------------------
 
 =head2 new
@@ -35,6 +57,110 @@ sub new {
   return $self;
 }
 
+#----------------------------------------------------------------------
+=head2 store_hsp
+
+  Arg [1]   : Bio::Search::HSP::EnsemblHSP obj
+  Function  : Stores the ensembl HSP in the database
+  Returntype: 
+  Exceptions: 
+  Caller    : 
+  Example   : 
+
+=cut
+
+sub store_hsp{
+  my $self = shift;
+  my $hsp  = shift || $self->throw( "Need an HSP obj" );
+  my $dbh  = $self->db->db_handle;
+
+  my $token = $hsp->token;
+
+  my( $rv );
+  if( $token ){
+    my $sth = $dbh->prepare( $SQL_HSP_RETRIEVE );
+    $rv = $sth->execute( $token ) ||  $self->throw( $sth->errstr );
+    $sth->finish;
+  }
+
+  my $store_obj = $hsp->_prepare_storable;
+  my $frozen = freeze( $store_obj );
+  my $ticket = $hsp->blast_ticket;
+
+  my $chr_name  = 'NULL';
+  my $chr_start = 'NULL';
+  my $chr_end   = 'NULL';
+  if( my $genomic = $hsp->genomic_hit ){
+    $chr_name  = $genomic->seq_id;
+    $chr_start = $genomic->start;
+    $chr_end   = $genomic->end;
+  } 
+
+  if( $rv ){ # Update
+    my $sth = $dbh->prepare( $SQL_HSP_UPDATE );
+    my @bound = ( $frozen, $chr_name,  $chr_start, $chr_end, $token );
+    $sth->execute( @bound ) || $self->throw( $sth->errstr );
+    $sth->finish;
+  }
+  else{ # Insert
+    my $sth = $dbh->prepare( $SQL_HSP_STORE );
+    my @bound = ( $ticket, $frozen, $chr_name,  $chr_start, $chr_end );
+    $sth->execute( @bound ) || $self->throw( $sth->errstr );
+    $hsp->token( $dbh->{mysql_insertid} );
+    $sth->finish;
+  }
+  return $hsp->token();
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve_hsp
+
+  Arg [1]   : 
+  Function  : 
+  Returntype: 
+  Exceptions: 
+  Caller    : 
+  Example   : 
+
+=cut
+
+sub retrieve_hsp{
+  my $self = shift;
+  my $dbh  = $self->db->db_handle;
+  my( $caller, $token ) = @_;
+  
+  my $hsp;
+  my $class = ref( $caller ) || $caller;
+
+  # Is this a call on a retrievable object?
+  if( ref( $caller ) ){
+    if( $caller->retrievable ){
+      $hsp = $caller;
+      $token = $hsp->token;
+    }
+  }
+  else{ $hsp = bless( {}, $caller ) }
+
+  if( ! $token ){ $self->throw( "Need an HSP token" ) }
+  my $sth = $dbh->prepare( $SQL_HSP_RETRIEVE );
+  my $rv  = $sth->execute( $token ) || $self->throw( $sth->errstr );
+  if( $rv < 1 ){ $self->throw( "Token $token not found" ) }
+  my ( $frozen ) = $sth->fetchrow_array;
+  $sth->finish;
+  my $stored_obj = thaw( $frozen );
+
+  if( ! ref( $stored_obj ) or 
+      ! $stored_obj->isa( 'Bio::Root::Storable' ) ){
+    $self->throw( "Token $token returned no data" );
+  }
+  $stored_obj->{-retrievable} = 0;
+  map{ $hsp->{$_} = $stored_obj->{$_} } keys %$stored_obj; # Copy hasheys
+  return bless( $hsp, ref( $stored_obj ) ); # Maintain class of stored obj
+
+}
+
+
 #----------------------------------------------------------------------
 
 =head2 get_all_HSPs
@@ -85,6 +211,7 @@ AND    chr_end   >= ? );
    my $rv = $sth->execute( @binded ) || $self->throw( $sth->errstr );
 
    my @hsps = map{ thaw( $_->[0] ) } @{$sth->fetchall_arrayref()};
+   $sth->finish;
 
    return [@hsps];
 }
@@ -107,11 +234,26 @@ AND    chr_end   >= ? );
 sub get_all_SearchFeatures {
   my $self = shift;
   my $hsps = $self->get_all_HSPs(@_);
+  $self->dynamic_use( ref($hsps->[0] ) );
   my @feats = grep{ $_ } map{ $_->ens_genomic_align } @$hsps;
   return [ @feats ];
 }
 
+#----------------------------------------------------------------------
 
+sub dynamic_use {
+  my( $self, $classname ) = @_;
+  my( $parent_namespace, $module ) = $classname =~/^(.*::)(.*?)$/;
+  no strict 'refs';
+  return 1 if $parent_namespace->{$module.'::'}; # return if already used
+  eval "require $classname";
+  if($@) {
+    warn "DrawableContainer: failed to use $classname\nDrawableContainer: $@";
+    return 0;
+  }
+  $classname->import();
+  return 1;
+}
 
 
 #----------------------------------------------------------------------