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Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor:

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Registry;

  ## Load adaptors using the Registry
  Bio::EnsEMBL::Registry-\>load_all();

  ## Fetch the query slice
  my $query_slice_adaptor = Bio::EnsEMBL::Registry-\>get_adaptor(
          "Homo sapiens", "core", "Slice");
  my $query_slice = $query_slice_adaptor-\>fetch_by_region(
          "chromosome", "14", 50000001, 50010001);

  ## Fetch the method_link_species_set
  my $mlss_adaptor = Bio::EnsEMBL::Registry-\>get_adaptor(
          "Compara26", "compara", "MethodLinkSpeciesSet");
  my $method_link_species_set = $mlss_adaptor-\>fetch_by_method_link_type_registry_aliases(
          "BLASTZ_NET", ["Homo sapiens", "Rattus norvegicus"]);

  ## Fetch the align_slice
  my $align_slice_adaptor = Bio::EnsEMBL::Registry-\>get_adaptor(
          "Compara26",
          "compara",
          "AlignSlice"
      );
  my $align_slice = $align_slice_adaptor-\>fetch_by_Slice_MethodLinkSpeciesSet(
          $query_slice,
          $method_link_species_set,
          "expanded"
      );

Definition at line 41 of file AlignSliceAdaptor.pm.

Available Methods

protected _columns ()
protected void _combine_genomic_align_trees ()
protected _default_where_clause ()
protected _final_clause ()
protected _get_right_node_id ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::AlignSlice 
fetch_by_GenomicAlignBlock ()
public
Bio::EnsEMBL::Compara::AlignSlice 
fetch_by_Slice_MethodLinkSpeciesSet ()
public void flush_cache ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor 
new ()
public DBI::StatementHandle prepare ()
public Int species_id ()

Method Documentation

protected void Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::_combine_genomic_align_trees ( )
  Arg[1]     : listref $species_order
  Arg[2]     : Bio::EnsEMBL::Compara::GenomicAlignTree $this_tree
  Arg[3]     : Bio::EnsEMBL::Compara::GenomicAlignTree $next_tree
  Example    :
  Description: This method tries to accommodate the nodes in $next_tree
               into $species_order. It uses several approaches. If there
               is information available about left and right node IDs, it
               will use it to link the nodes. Alternatively, it will rely
               on the species names to do its best. When a new species name
               appears in the $next_tree, it will try to insert it in the right
               position.
  Returntype : none
  Exceptions : none
  Caller     : $object->methodname
 
Code:
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protected Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::_get_right_node_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::AlignSlice Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_GenomicAlignBlock ( )
  Arg[1]     : Bio::EnsEMBL::Compara::GenomicAlignBlock $genomic_align_block
  Arg[2]     : [optional] boolean $expanded (def. FALSE)
  Arg[3]     : [optional] boolean $solve_overlapping (def. FALSE)
  Example    :
      my $align_slice = $align_slice_adaptor->fetch_by_GenomicAlignBlock(
              $genomic_align_block);
  Description: Uses this genomic_aling_block to create an AlignSlice.
               Setting $expanded to anything different
               from 0 or "" will create an AlignSlice in "expanded" mode. This means
               that gaps are allowed in the reference species in order to allocate
               insertions from other species.
               By default overlapping alignments are ignored. You can choose to
               reconciliate the alignments by means of a fake alignment setting the
               solve_overlapping option to TRUE.
  Returntype : Bio::EnsEMBL::Compara::AlignSlice
  Exceptions : thrown if arg[1] is not a Bio::EnsEMBL::Compara::GenomicAlignBlock
  Exceptions : thrown if $genomic_align_block has no method_link_species_set
  Caller     : $object->methodname
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_Slice_MethodLinkSpeciesSet ( )
  Arg[1]     : Bio::EnsEMBL::Slice $query_slice
  Arg[2]     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Arg[3]     : [optional] boolean $expanded (def. FALSE)
  Arg[4]     : [optional] boolean $solve_overlapping (def. FALSE)
  Arg[5]     : [optional] Bio::EnsEMBL::Slice $target_slice
  Example    :
      my $align_slice = $align_slice_adaptor->fetch_by_Slice_MethodLinkSpeciesSet(
              $query_slice, $method_link_species_set);
  Description: Fetches from the database all the data needed for the AlignSlice
               corresponding to the $query_slice and the given
               $method_link_species_set. Setting $expanded to anything different
               from 0 or "" will create an AlignSlice in "expanded" mode. This means
               that gaps are allowed in the reference species in order to allocate
               insertions from other species.
               By default overlapping alignments are ignored. You can choose to
               reconciliate the alignments by means of a fake alignment setting the
               solve_overlapping option to TRUE.
               In order to restrict the AlignSlice to alignments with a given
               genomic region, you can specify a target_slice. All alignments which
               do not match this slice will be ignored.
  Returntype : Bio::EnsEMBL::Compara::AlignSlice
  Exceptions : thrown if wrong arguments are given
  Caller     : $object->methodname
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::flush_cache ( )
  Arg[1]     : none
  Example    : $align_slice_adaptor->flush_cache()
  Description: Destroy the cache
  Returntype : none
  Exceptions : none
  Caller     : $object->methodname
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::new ( )
  Arg        : 
  Example    : 
  Description: Creates a new AlignSliceAdaptor object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::Registry->get_adaptor
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.


The documentation for this class was generated from the following file: