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Bio::EnsEMBL::Compara::SyntenyRegion Class Reference

List of all members.


Class Summary

Synopsis

  print $this_synteny_region-\>dbID;

  print $this_synteny_region-\>method_link_species_set_id;

  my $these_dnafrag_regions = $this_synteny_region-\>get_all_DnaFragRegions();
  foreach my $this_dnafrag_region (@$these_dnafrag_regions) {
    print $this_dnafrag_region-\>genome_db-\>name, ": ", $this_dnafrag_region-\>slice-\>name, "\n";
  }

Description

A Bio::EnsEMBL::Compara::SyntenyRegion object is a container of Bio::EnsEMBL::Compara::DnaFragRegion
objects. Each Bio::EnsEMBL::Compara::DnaFragRegion represent a genomic region which is in synteny
with the other regions represented in the Bio::EnsEMBL::Compara::SyntenyRegion object.
Also, the Bio::EnsEMBL::Compara::SyntenyRegion object implicitly contains a
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object which defines the type of synteny.
 

Definition at line 29 of file SyntenyRegion.pm.

Available Methods

public
Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor 
adaptor ()
public Int dbID ()
public A get_all_DnaFragRegions ()
public Int method_link_species_set_id ()
public
Bio::EnsEMBL::Compara::SyntenyRegion 
new_fast ()
public
Bio::EnsEMBL::Compara::SyntenyRegion 
new_fast ()
public regions ()
public stable_id ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor Bio::EnsEMBL::Compara::SyntenyRegion::adaptor ( )
  Arg [1]     : (optional) Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor $adaptor
  Example     : none
  Description : Getter/setter for the adaptor
  Returntype  : Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::SyntenyRegion::dbID ( )
  Arg [1]     : (optional) integer $dbID
  Example     : none
  Description : Getter/setter for the dbID value. This corresponds to
                synteny_region.synteny_region_id
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public A Bio::EnsEMBL::Compara::SyntenyRegion::get_all_DnaFragRegions ( )
 Arg  1     : -none-
 Example    : my $all_dnafrag_regions = $obj->get_all_DnaFragRegions();
 Description: returns all the DnaFragRegion objects for this syntenic
              region. This method is an alias for children(), see
              Bio::EnsEMBL::Compara::NestedSet for more details.
 Returntype : a ref. to an array of Bio::EnsEMBL::Compara::DnaFragRegion
              objects
 Exception  :
 Caller     : general
 Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::SyntenyRegion::method_link_species_set_id ( )
  Arg [1]     : (optional) integer $method_link_species_set_id
  Example     : none
  Description : Getter/setter for the method_link_species_set_id value.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
public Bio::EnsEMBL::Compara::SyntenyRegion Bio::EnsEMBL::Compara::SyntenyRegion::new_fast ( )
  Arg [-DBID] : integer $dbID
  Arg [-METHOD_LINK_SPECIES_SET_ID]
              : integer $method_link_species_set_id
  Arg [-ADAPTOR]
              : Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor $adaptor
  Example     : none
  Description : This is the default constructor
  Returntype  : Bio::EnsEMBL::Compara::SyntenyRegion object
  Exceptions  : none
  Caller      :
  Status      : Stable
 
Code:
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  Arg [1]     : hash reference $hashref
  Example     : none
  Description : This is an ultra fast constructor which requires knowledge of
                the objects internals to be used.
  Returntype  : Bio::EnsEMBL::Compara::SyntenyRegion object
  Exceptions  : none
  Caller      :
  Status      : Stable
 
Code:
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public Bio::EnsEMBL::Compara::SyntenyRegion Bio::EnsEMBL::Compara::SyntenyRegion::new_fast ( )
public Bio::EnsEMBL::Compara::SyntenyRegion::regions ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::SyntenyRegion::stable_id ( )
Deprecated:
: SyntenyRegions don't have any stable id.
 
Code:
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The documentation for this class was generated from the following file: