added several fetch methods, fixed some small bugs in store method

modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm

@@ -6,21 +6,6 @@
 #
 # You may distribute this module under the same terms as perl itself
 
-# POD documentation - main docs before the code
-
-
-
-
-#mysql> desc density_type;
-#+-----------------+---------------------+------+-----+---------+----------------+
-#| Field           | Type                | Null | Key | Default | Extra          |
-#+-----------------+---------------------+------+-----+---------+----------------+
-#| density_type_id | int(11)             |      | PRI | NULL    | auto_increment |
-#| analysis_id     | int(11)             |      | MUL | 0       |                |
-#| block_size      | int(11)             |      |     | 0       |                |
-#| value_type      | enum('sum','ratio') |      |     | sum     |                |
-#+-----------------+---------------------+------+-----+---------+----------------+
-
 =head1 NAME
 
 Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
@@ -28,13 +13,14 @@ Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
 =head1 SYNOPSIS
 
 my $density_type_adaptor = $database_adaptor->get_DensityTypeAdaptor();
-@density_types = @{$density_type_adaptor->fetch_all_by_Slice($slice)};
+@density_types = @{$density_type_adaptor->fetch_all()};
 
-=head1 DESCRIPTION
+my $dt = $density_type_adaptor->fetch_by_dbID(12);
 
-Simple Feature Adaptor - database access for simple features
 
-=head1 AUTHOR - Ewan Birney
+=head1 DESCRIPTION
+
+DensityTypeAdaptor - Performs database interaction for DensityType objects.
 
 =head1 METHODS
 
@@ -44,11 +30,177 @@ package Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
 use vars qw(@ISA);
 use strict;
 
-use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
-#use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+
+use Bio::EnsEMBL::DensityType;
 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 
-@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+
+
+=head2 new
+
+  Arg [1]    : see superclass (Bio::EnsEMBL::DBSQL::BaseAdaptor) arguments
+  Example    : #use this instead of the constructor directly:
+               my $dta = $db_adaptor->get_DensityTypeAdaptor();
+  Description: Constructor. Creates a new DensityTypeAdaptor
+  Returntype : Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
+  Exceptions : none
+  Caller     : DBAdaptor
+
+=cut
+
+sub new {
+  my $class = shift;
+
+  my $self = $class->SUPER::new(@_);
+
+  $self->{'dbID_cache'} = {};
+
+  return $self;
+}
+
+
+
+=head2 fetch_all
+
+  Arg [1]    : none
+  Example    : my @density_types = @{$density_type_adaptor->fetch_all};
+  Description: Retrieves every density type in the database
+  Returntype : reference to list of Bio::EnsEMBL::DensityType objects
+  Exceptions : none
+  Caller     : general, new
+
+=cut
+
+sub fetch_all {
+  my $self = shift;
+
+  my @out;
+
+  my $sth = $self->prepare("SELECT density_type_id, analysis_id, block_size,".
+                           "       value_type " .
+                           "FROM density_type");
+
+  $sth->execute();
+
+  my($dbID, $analysis_id, $blk_size, $vtype);
+  $sth->bind_columns(\$dbID, \$analysis_id, \$blk_size, \$vtype);
+
+  my $analysis_adaptor = $self->db->get_AnalysisAdaptor();
+
+  while($sth->fetch()) {
+    my $analysis = $analysis_adaptor->fetch_by_dbID($analysis_id);
+
+    my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
+                                            -DBID    => $dbID,
+                                            -ANALYSIS => $analysis,
+                                            -BLOCK_SIZE => $blk_size,
+                                            -VALUE_TYPE => $vtype);
+
+    $self->{'dbID_cache'}->{$dbID} = $dt;
+
+    push @out, $dt;
+  }
+
+  return \@out;
+}
+
+
+
+=head2 fetch_by_dbID
+
+  Arg [1]    : int $dbID
+  Example    : my $dt = $density_type_adaptor->fetch_by_dbID($dbID);
+  Description: Retrieves a density type object via its internal identifier
+  Returntype : Bio::EnsEMBL::DensityType
+  Exceptions : throw if dbID argument not defined
+  Caller     : general
+
+=cut
+
+sub fetch_by_dbID {
+  my $self = shift;
+  my $dbID = shift;
+
+  if(!defined($dbID)) {
+    throw("dbID argument must be defined");
+  }
+
+  if($self->{'dbID_cache'}->{$dbID}) {
+    return $self->{'dbID_cache'}->{$dbID};
+  }
+
+  # go back to database and refill caches
+  $self->fetch_all();
+
+  return $self->{'dbID_cache'}->{$dbID};
+}
+
+
+=head2 fetch_all_by_logic_name
+
+  Arg [1]    : string $logic_name
+  Example    : my @dts = @{$dtype_adaptor->fetch_all('repeat_coverage')};
+  Description: Retrieves all density types with a given logic name
+  Returntype : reference to list of Bio::EnsEMBL::DensityTypes
+  Exceptions : thrown if logic_name argument is not provided
+  Caller     : general
+
+=cut
+
+sub fetch_all_by_logic_name {
+  my $self = shift;
+  my $logic_name = shift;
+
+  if(!defined($logic_name)) {
+    throw("logic_name argument is required.");
+  }
+
+  my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
+
+  my $analysis = $analysis_adaptor->fetch_by_logic_name($logic_name);
+
+  return [] if(!$analysis);
+
+  my $sth = $self->prepare("SELECT density_type_id, block_size,".
+                           "       value_type " .
+                           "FROM density_type " .
+                           "WHERE analysis_id = ?");
+  $sth->execute($analysis->dbID());
+
+  my($dbID, $blk_size, $vtype);
+  $sth->bind_columns(\$dbID, \$blk_size, \$vtype);
+
+  my @out;
+
+  while($sth->fetch()) {
+    my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
+                                            -DBID    => $dbID,
+                                            -ANALYSIS => $analysis,
+                                            -BLOCK_SIZE => $blk_size,
+                                            -VALUE_TYPE => $vtype);
+
+    $self->{'dbID_cache'}->{$dbID} = $dt;
+
+    push @out, $dt;
+  }
+
+  return \@out;
+}
+
+
+#
+# garbage collection method, automatically called when DBAdaptor is cleaned up
+#
+sub deleteObj {
+  my $self = shift;
+
+  delete $self->{'dbID_cache'};
+
+  $self->SUPER::deleteObj;
+}
 
 
 =head2 store
@@ -63,17 +215,8 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
   Caller     : general
 
 =cut
-#mysql> desc density_type;
-#+-----------------+---------------------+------+-----+---------+----------------+
-#| Field           | Type                | Null | Key | Default | Extra          |
-#+-----------------+---------------------+------+-----+---------+----------------+
-#| density_type_id | int(11)             |      | PRI | NULL    | auto_increment |
-#| analysis_id     | int(11)             |      | MUL | 0       |                |
-#| block_size      | int(11)             |      |     | 0       |                |
-#| value_type      | enum('sum','ratio') |      |     | sum     |                |
-#+-----------------+---------------------+------+-----+---------+----------------+
-
-sub store{
+
+sub store {
   my ($self,@dt) = @_;
 
   if( scalar(@dt) == 0 ) {
@@ -89,39 +232,36 @@ sub store{
   my $analysis_adaptor = $db->get_AnalysisAdaptor();
 
  FEATURE: foreach my $dt ( @dt ) {
-    
     if( !ref $dt || !$dt->isa("Bio::EnsEMBL::DensityType") ) {
       throw("Density Type must be an Ensembl DensityType, " .
             "not a [".ref($dt)."]");
     }
-    
+
     if($dt->is_stored($db)) {
       warning("DensityType [".$dt->density_type_id."] is already stored" .
               " in this database.");
       next FEATURE;
     }
-    
-    if(!defined($dt->analysis)) {
+
+    if(!defined($dt->analysis())) {
       throw("An analysis must be attached to the density type to be stored.");
     }
-    
+
     #store the analysis if it has not been stored yet
     if(!$dt->analysis->is_stored($db)) {
-      throw("Analysis must already exist???? But does not??");
+      $analysis_adaptor->store($dt->analysis());
     }
 	
+    $sth->execute($dt->analysis->dbID(), $dt->block_size(), $dt->value_type());
 
-    $sth->execute($dt->analysis->dbID,
-		  $dt->{'block_size'}, $dt->{'value_type'});
-
+    my $dbID = $sth->{'mysql_insertid'};
 
     # next two lines are to set the density type as stored
-    $dt->dbID($sth->{'mysql_insertid'});
+    $dt->dbID($dbID);
     $dt->adaptor($self);
+
+    $self->{'dbID_cache'}->{$dbID} = $dt;
   }
 }
 
-    
-    
-   
-
+1;