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Summary

Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor - Object to access data in genomic_align_group table

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::BaseAdaptor

Synopsis

  use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor; 
  my $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor (
      -host => $host,
      -user => $dbuser,
      -pass => $dbpass,
      -port => $port,
      -dbname => $dbname,
      -conf_file => $conf_file);
  
  my $genomic_align_group_adaptor = $db->get_GenomicAlignGroupAdaptor();

  $genomic_align_group_adaptor->store($genomic_align_group);

  $genomic_align_groups = $genomic_align_group_adaptor->fetch_all_by_GenomicAlign($genomic_align);
  $genomic_align_groups = $genomic_align_group_adaptor->fetch_all_by_genomic_align_id(11223);

  $genomic_align_group = $genomic_align_group_adaptor->fetch_by_GenomicAlign_type($genomic_align,
      "default");
  $genomic_align_group = $genomic_align_group_adaptor->fetch_by_genomic_align_id_type(11223,
      "default");

Description

This class is intended to access data in genomic_align_group table

Methods

Methods description

  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : my $genomic_align_groups =
                  $genomic_align_group_adaptor->fetch_all_by_GenomicAlign(
                          $genomic_align)
  Description: Returns all the  Bio::EnsEMBL::Compara::GenomicAlignGroup
               corresponding to the given Bio::EnsEMBL::Compara::GenomicAlign.
  Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignGroup
               objects.
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable

  Arg  1     : integer $genomic_align_id
  Example    : my $genomic_align_groups =
                  $genomic_align_group_adaptor->fetch_all_by_genomic_align_id(
                          124214)
  Description: Returns all the  Bio::EnsEMBL::Compara::GenomicAlignGroup
               corresponding to the given Bio::EnsEMBL::Compara::GenomicAlign.
  Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignGroup
               objects.
  Exceptions : none
  Caller     : object->methodname
  Status     : Stable

  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Arg  2     : string $genomic_align_group_type
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_GenomicAlign_and_type(
                          $genomic_align, "default")
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given Bio::EnsEMBL::Compara::GenomicAlign and group_type.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable

  Arg  1     : integer group_id
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_dbID(12413)
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given group_id.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable

  Arg  1     : integer $genomic_align_id
  Arg  2     : string $genomic_align_group_type
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_genomic_align_id_type(
                          12322, "default")
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given Bio::EnsEMBL::Compara::GenomicAlign defined by the
               $genomic_align_id and to the group_type.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable

  Arg [1]    : list of args to super class constructor
  Example    : $gag_a = new Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor($dbobj);
  Description: Creates a new GenomicAlignGroupAdaptor. This
               class should be instantiated through the get method on the 
               DBAdaptor rather than calling this method directly.
  Returntype : none
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable

  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignGroup $genomic_align_group
  Example    : $genomic_align_group_adaptor->retrieve_all_direct_attributes($genomic_align_group)
  Description: Retrieve the all the direct attibutes corresponding to the dbID of the
               Bio::EnsEMBL::Compara::GenomicAlignGroup object. It is used after lazy fetching
               of the object for populating it when required.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : 
  Caller     : none
  Status     : Stable

  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignGroup
               The things you want to store
  Example    : $gen_ali_grp_adaptor->store($genomic_align_group);
  Description: It stores the given GenomicAlginGroup in the database
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup object
  Exceptions : not stored linked Bio::EnsEMBL::Compara::GenomicAlign objects throw.
  Caller     : general
  Status     : Stable

  [Arg  1]   : (optional)int value
  Example    : $genomic_align_adaptor->use_autoincrement(0);
  Description: Getter/setter for the _use_autoincrement flag. This flag
               is used when storing new objects with no dbID in the
               database. If the flag is ON (default), the adaptor will
               let the DB set the dbID using the AUTO_INCREMENT ability.
               If you unset the flag, then the adaptor will look for the
               first available dbID after 10^10 times the
               method_link_species_set_id.
  Returntype : integer
  Exceptions : 
  Caller     : none
  Status     : Stable

Methods code

sub fetch_all_by_GenomicAlign {

  my ($self, $genomic_align) = @_;
  my $genomic_align_groups = [];

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
  
  # Check Bio::EnsEMBL::Compara::GenomicAlign object
  unless($genomic_align && ref $genomic_align && 
        $genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
    throw("genomic_align argument must be a Bio::EnsEMBL::Compara::GenomicAlign not a [$genomic_align]");
  }

  my $genomic_align_block_sql = qq{
              SELECT
                group_id,
                type
              FROM
                genomic_align_group
              WHERE
                genomic_align_id = ?
        };
  
  my $sth = $self->prepare($genomic_align_block_sql);
  $sth->execute($genomic_align->dbID);


  my $groups;
  while (my $values = $sth->fetchrow_arrayref) {
    my ($group_id, $type) = @$values;

    $groups->{$group_id}->{'type'} = $type;
  }

  foreach my $group_id (keys %$groups) {
    my $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
            -dbID => $group_id,
            -adaptor => $self,
            -type => $groups->{$group_id}->{'type'},
        );
    push(@{$genomic_align_groups}, $genomic_align_group);
  }

  return $genomic_align_groups;

}

sub fetch_all_by_genomic_align_id {

  my ($self, $genomic_align_id) = @_;
  my $genomic_align_groups = [];

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
  
  my $genomic_align_block_sql = qq{
              SELECT
                group_id,
                type
              FROM
                genomic_align_group
              WHERE
                genomic_align_id = ?
        };
  
  my $sth = $self->prepare($genomic_align_block_sql);
  $sth->execute($genomic_align_id);


  my $groups;
  while (my $values = $sth->fetchrow_arrayref) {
    my ($group_id, $type) = @$values;

    $groups->{$group_id}->{'type'} = $type;
  }

  foreach my $group_id (keys %$groups) {
    my $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
            -dbID => $group_id,
            -adaptor => $self,
            -type => $groups->{$group_id}->{'type'},
        );
    push(@{$genomic_align_groups}, $genomic_align_group);
  }

  return $genomic_align_groups;
}

# # =head2 fetch_by_GenomicAlign_and_type
# # 
# #   Arg  1     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
# #                       - or -
# #                integer $genomic_align_id
# #   Arg  2     : string $genomic_align_group_type
# #   Example    : my $genomic_align_group =
# #                   $genomic_align_group_adaptor->fetch_by_GenomicAlign_and_type(
# #                           $genomic_align, "default")
# #   Example    : my $genomic_align_groups =
# #                   $genomic_align_group_adaptor->fetch_all_by_GenomicAlign(
# #                           124214, "default")
# #   Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
# #                to the given Bio::EnsEMBL::Compara::GenomicAlign and group_type.
# #   Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
# #   Exceptions : none
# #   Caller     : object::methodname
# # 
# # =cut

}

sub fetch_by_GenomicAlign_and_type {

  my ($self, $genomic_align, $type) = @_;
  my $genomic_align_group;

  deprecate("Use fetch_by_GenomicAlign_type method instead");

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;

  # Get Bio::EnsEMBL::Compara::GenomicAlign object from dbID if needed
  if ($genomic_align =~ /^\d+$/) {
    $genomic_align = $genomic_align_adaptor->fetch_by_dbID($genomic_align);
  }

  return $self->fetch_by_GenomicAlign_type($genomic_align, $type);

}

sub fetch_by_GenomicAlign_type {

  my ($self, $genomic_align, $type) = @_;
  my $genomic_align_group;

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
  
  # Check Bio::EnsEMBL::Compara::GenomicAlign object
  unless($genomic_align && ref $genomic_align && 
        $genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
    throw("[$genomic_align] must be a Bio::EnsEMBL::Compara::GenomicAlign object");
  }

  my $genomic_align_block_sql = qq{
              SELECT
                  b.group_id,
                  b.type,
                  b.genomic_align_id
              FROM
                genomic_align_group a, genomic_align_group b
              WHERE
                a.group_id = b.group_id
                AND a.genomic_align_id = ?
                AND a.type = ?
        };
  
  my @values;
  
  my $sth = $self->prepare($genomic_align_block_sql);
  $sth->execute($genomic_align->dbID, $type);

  # Group results in order to be able to build Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor objects
  my $group;
  while (my $values = $sth->fetchrow_arrayref) {
    my ($group_id, $type, $genomic_align_id) = @$values;

    $group->{'group_id'} = $group_id;
    $group->{'type'} = $type;
    my $this_genomic_align;
    if ($genomic_align_id == $genomic_align->dbID) {
      # Use Bio::EnsEMBL::Compara::GenomicAlign object given by argument if possible
      $this_genomic_align = $genomic_align;
    } else {
      # Create a new Bio::EnsEMBL::Compara::GenomicAlign object otherwise
      $this_genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
              -dbID => $genomic_align_id,
              -adaptor => $genomic_align_adaptor
          );
    }

    push(@{$group->{'genomic_align_array'}}, $this_genomic_align);
  }

  $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
          -dbID => $group->{'group_id'},
          -adaptor => $self,
          -type => $group->{'type'},
          -genomic_align_array => $group->{'genomic_align_array'}
      );
  foreach my $this_genomic_align (@{$genomic_align_group->genomic_align_array}) {
    $this_genomic_align->genomic_align_group_by_type($genomic_align_group->type, $genomic_align_group);
  }

  return $genomic_align_group;

}

sub fetch_by_dbID {

  my ($self, $group_id) = @_;
  my $genomic_align_group;

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
  
  my $genomic_align_block_sql = qq{
              SELECT
                  group_id,
                  type,
                  genomic_align_id
              FROM
                genomic_align_group
              WHERE
                group_id = ?
        };
  
  my @values;
  
  my $sth = $self->prepare($genomic_align_block_sql);
  $sth->execute($group_id);

  # Group results in order to be able to build Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor objects
  my $group;
  while (my $values = $sth->fetchrow_arrayref) {
    my ($group_id, $type, $genomic_align_id) = @$values;

    $group->{'group_id'} = $group_id;
    $group->{'type'} = $type;
    my $this_genomic_align = new Bio::EnsEMBL::Compara::GenomicAlign(
            -dbID => $genomic_align_id,
            -adaptor => $genomic_align_adaptor
        );

    push(@{$group->{'genomic_align_array'}}, $this_genomic_align);
  }

  #return undef if no genomic_align_groups have been found
  if (!defined $group->{'group_id'}) {
      return $genomic_align_group;
  }

  $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup(
          -dbID => $group->{'group_id'},
          -adaptor => $self,
          -type => $group->{'type'},
          -genomic_align_array => $group->{'genomic_align_array'}
      );
  foreach my $this_genomic_align (@{$genomic_align_group->genomic_align_array}) {
    $this_genomic_align->genomic_align_group_by_type($genomic_align_group->type, $genomic_align_group);
  }

  return $genomic_align_group;

}

sub fetch_by_genomic_align_id_type {

  my ($self, $genomic_align_id, $type) = @_;
  my $genomic_align_group;

  my $genomic_align_adaptor = $self->db->get_GenomicAlignAdaptor;
  
  # Get Bio::EnsEMBL::Compara::GenomicAlign object
  my $genomic_align = $genomic_align_adaptor->fetch_by_dbID($genomic_align_id);
  unless($genomic_align && ref $genomic_align && 
        $genomic_align->isa('Bio::EnsEMBL::Compara::GenomicAlign')) {
    throw("[$genomic_align] must be a Bio::EnsEMBL::Compara::GenomicAlign object");
  }

  return $self->fetch_by_GenomicAlign_type($genomic_align, $type);

}

sub new {

  my $class = shift;

  my $self = $class->SUPER::new(@_);

  $self->{_use_autoincrement} = 1;

  return $self;

}

sub retrieve_all_direct_attributes {

  my ($self, $genomic_align_group) = @_;

  my $sql_tmp = "SELECT type FROM genomic_align_group WHERE group_id = ?";
  my $sql = $self->dbc->add_limit_clause($sql_tmp,1);
#   my $sql = qq{
#                 SELECT
#                     type
#                 FROM
#                     genomic_align_group
#                 WHERE
#                     group_id = ?
#                 LIMIT 1
#         };

  my $sth = $self->prepare($sql);
  $sth->execute($genomic_align_group->dbID);
  my ($type) = $sth->fetchrow_array();
  
  ## Populate the object
  $genomic_align_group->adaptor($self);
  $genomic_align_group->type($type) if (defined($type));

  return $genomic_align_group;

}

sub store {

  my ($self, $genomic_align_group) = @_;

  my $genomic_align_block_sql =
        qq{INSERT INTO genomic_align_group (
                group_id,
                type,
                genomic_align_id
        ) VALUES (?,?,?)};
  
  my @values;
  
  ## CHECKING
  my $all_genomic_aligns = $genomic_align_group->get_all_GenomicAligns;
  foreach my $genomic_align (@$all_genomic_aligns) {
    # check if every GenomicAlgin has a dbID
    if (!defined($genomic_align->dbID)) {
      throw("GenomicAlign [$genomic_align] in GenomicAlignGroup is not in DB");
    }
  }
  
  my $group_id = $genomic_align_group->dbID;
  if (!$group_id) {
    my $method_link_species_set_id;
    # Get common method_link_species_set_id
    foreach my $genomic_align (@$all_genomic_aligns) {
      if (!$genomic_align->method_link_species_set_id()) {
        ## undef value and exit loop if method_link_species_set_id does not match
        $method_link_species_set_id = undef;
        last;
      } elsif (!$method_link_species_set_id) {
        $method_link_species_set_id = $genomic_align->method_link_species_set_id();
      } elsif ($method_link_species_set_id != $genomic_align->method_link_species_set_id()) {
        ## undef value and exit loop if method_link_species_set_id does not match
        $method_link_species_set_id = undef;
        last;
      }
    }
    if ($method_link_species_set_id && !$self->use_autoincrement()) {
      ## Only if method_link_species_set_id is the same for all the GenomicAligns
      my $sql = 
              "SELECT MAX(group_id) FROM genomic_align_group WHERE".
              " group_id > ".$method_link_species_set_id.
              "0000000000 AND group_id < ".
              ($method_link_species_set_id + 1)."0000000000";
      my $sth = $self->prepare($sql);
      $sth->execute();
      $group_id = $sth->fetchrow_array();
      if (defined $group_id) {
        $group_id++;
      } else {
        $group_id = $method_link_species_set_id * 10000000000 + 1;
      }
    }
  }

  ## Stores data, all of them with the same id
  my $sth = $self->prepare($genomic_align_block_sql);
  for (my $i = 0; $i < @$all_genomic_aligns; $i++) {
    my $genomic_align  = $all_genomic_aligns->[$i];
    $sth->execute(
                  ($group_id or "NULL"),
                  $genomic_align_group->type,
                  $genomic_align->dbID
          );
    if (!$group_id) {$group_id = $sth->{'mysql_insertid'};}

    info("Stored Bio::EnsEMBL::Compara::GenomicAlignGroup ".
          "(".($i+1)."/".scalar(@$all_genomic_aligns).") ".
          ($group_id or "NULL").", ".$genomic_align_group->type.", ".
          $genomic_align->dbID, );

  }
  $genomic_align_group->dbID($group_id);
  
  return $genomic_align_group;

}

sub use_autoincrement {

  my ($self, $value) = @_;

  if (defined $value) {
    $self->{_use_autoincrement} = $value;
  }

  return $self->{_use_autoincrement};
}

1;

}

General documentation

Javier Herrero (jherrero@ebi.ac.uk)
This modules is part of the Ensembl project

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _