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Bio::EnsEMBL::Compara::DnaFragRegion Class Reference

List of all members.


Class Summary

Synopsis

  my $slice = $dnafrag_region-\>slice;
  my $dnafrag = $dnafrag_region-\>dnafrag;
  my $genome_db = $dnafrag_region-\>genome_db;
  my $dnafrag_start = $dnafrag_region-\>dnafrag_start;
  my $dnafrag_end = $dnafrag_region-\>dnafrag_end;
  my $dnafrag_strand = $dnafrag_region-\>dnafrag_strand;
  my $length = $dnafrag_region-\>length;

Description

DnaFragRegion are the objects underlying the SyntenyRegion objects. Each synteny is
represented as a Bio::EnsEMBL::Compara::SyntenyRegion object. Each of these objects
contain one Bio::EnsEMBL::Compara::DnaFragRegion object per region which defines the
synteny. For instance, for a syntenic region between human and mouse, there will be
one DnaFragRegion object for the human region and another one for the mouse one.
 

Definition at line 27 of file DnaFragRegion.pm.

Available Methods

public
Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor 
adaptor ()
public
Bio::EnsEMBL::Compara::Dnafrag 
dnafrag ()
public Int dnafrag_end ()
public Int dnafrag_id ()
public Int dnafrag_start ()
public Int dnafrag_strand ()
public
Bio::EnsEMBL::Compara::GenomeDB 
genome_db ()
public Int length ()
public
Bio::EnsEMBL::Compara::DnaFragRegion 
new_fast ()
public
Bio::EnsEMBL::Compara::DnaFragRegion 
new_fast ()
public Bio::EnsEMBL::Slice slice ()
public Int synteny_region_id ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor Bio::EnsEMBL::Compara::DnaFragRegion::adaptor ( )
  Arg 1       : (optional) Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor $adaptor
  Example     : my $adaptor = $dnafrag->adaptor;
  Description : Getter/setter for the corresponding
                Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
  Returntype  : Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
  Exceptions  : none
  Caller      : general
 
Code:
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public Bio::EnsEMBL::Compara::Dnafrag Bio::EnsEMBL::Compara::DnaFragRegion::dnafrag ( )
  Arg 1       : (optional) Bio::EnsEMBL::Compara::DnaFrag object
  Example     : $dnafrag = $dnafragregion->dnafrag;
  Description : Getter/setter for the Bio::EnsEMBL::Compara::DnaFrag object corresponding to this
                Bio::EnsEMBL::Compara::DnaFragRegion object.
  Returntype  : Bio::EnsEMBL::Compara::Dnafrag object
  Exceptions  : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
                coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
                cannot be retrieved and returns undef.
  Caller      : $object->methodname
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::dnafrag_end ( )
  Arg 1       : (optional) integer $dnafrag_end
  Example     : my $dnafrag_end = $dnafrag->dnafrag_end;
  Description : Getter/setter for the dnafrag_end attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::dnafrag_id ( )
  Arg 1       : (optional) integer $dnafrag_id
  Example     : my $dnafrag_id = $dnafrag->dnafrag_id;
  Description : Getter/setter for the dnafrag_id attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::dnafrag_start ( )
  Arg 1       : (optional) integer $dnafrag_start
  Example     : my $dnafrag_start = $dnafrag->dnafrag_start;
  Description : Getter/setter for the dnafrag_start attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::dnafrag_strand ( )
  Arg 1       : (optional) integer $dnafrag_strand
  Example     : my $dnafrag_strand = $dnafrag->dnafrag_strand;
  Description : Getter/setter for the dnafrag_strand attribute
  Returntype  : integer (1 or -1)
  Exceptions  : none
  Caller      : general
 
Code:
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public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::DnaFragRegion::genome_db ( )
  Arg 1       : -none-
  Example     : $genome_db = $dnafragregion->genome_db;
  Description : Returns the Bio::EnsEMBL::Compara::GenomeDB object corresponding to this
                Bio::EnsEMBL::Compara::DnaFragRegion object. This method is a shortcut
                for $dnafragregion->dnafrag->genome_db
  Returntype  : Bio::EnsEMBL::Compara::GenomeDB object
  Exceptions  : return undef if no dnafrag can be found for this DnaFragRegion object.
                See dnafrag method elsewhere in this document.
  Caller      : $object->methodname
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::length ( )
  Arg 1       : -none-
  Example     : $length = $dnafragregion->length;
  Description : Returns the lenght of this DnaFragRegion
  Returntype  : integer
  Exceptions  :
  Caller      : $object->methodname
 
Code:
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public Bio::EnsEMBL::Compara::DnaFragRegion Bio::EnsEMBL::Compara::DnaFragRegion::new_fast ( )
  Arg         : possible keys: ADAPTOR, SYNTENY_REGION_ID, DNAFRAG_ID,
                DNAFRAG_START, DNAFRAG_END, DNAFRAG_STRAND
                See also parent object: Bio::EnsEMBL::Compara::NestedSet
  Example     : none
  Description : Object constructor.
  Returntype  : Bio::EnsEMBL::Compara::DnaFragRegion object
  Exceptions  : none
  Caller      : general
 
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::DnaFragRegion object
  Exceptions  : none
  Caller      : general
 
Code:
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public Bio::EnsEMBL::Compara::DnaFragRegion Bio::EnsEMBL::Compara::DnaFragRegion::new_fast ( )
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::DnaFragRegion::slice ( )
  Arg 1       : -none-
  Example     : $slice = $dnafragregion->slice;
  Description : Returns the Bio::EnsEMBL::Slice object corresponding to this
                Bio::EnsEMBL::Compara::DnaFrag object.
  Returntype  : Bio::EnsEMBL::Slice object
  Exceptions  : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
                coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
                cannot be retrieved and returns undef.
  Caller      : $object->methodname
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFragRegion::synteny_region_id ( )
  Arg 1       : (optional) integer $synteny_region_id
  Example     : my $synteny_region_id = $dnafrag->synteny_region_id;
  Description : Getter/setter for the synteny_region_id attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
 
Code:
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The documentation for this class was generated from the following file: