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Bio::EnsEMBL::Compara::SitewiseOmega Class Reference

List of all members.


Class Summary

Description

 

Synopsis

Give standard usage here

Description

Describe the object here
 

Definition at line 20 of file SitewiseOmega.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor 
adaptor ()
public Int aln_position ()
public dbID ()
public Int member_position ()
public new_fast ()
public node_id ()
public Int omega ()
public Float omega_lower ()
public Float omega_upper ()
public Float optimal ()
public Float threshold_on_branch_ds ()
public tree_node_id ()
public Int type ()

Method Documentation

public Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor Bio::EnsEMBL::Compara::SitewiseOmega::adaptor ( )
  Arg [1]    : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor $adaptor
  Example    : $sitewise_omega->adaptor($adaptor);
  Description: Getter/Setter for the adaptor this object used for database
               interaction
  Returntype : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
  Exceptions : thrown if the argument is not a
               Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
  Caller     : general
  Status     : At risk
 
Code:
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public Int Bio::EnsEMBL::Compara::SitewiseOmega::aln_position ( )
  Arg [1]    : (opt) integer
  Example    : $sitewise_dnds->aln_position(1);
  Description: Getter/Setter for the alignment position
  Returntype : integer. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::SitewiseOmega::dbID ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::Compara::SitewiseOmega::member_position ( )
  Arg [1]    : Bio::EnsEMBL::Member $member
  Arg [2]    : Bio::SimpleAlign $aln
  Example    : $sitewise_omega->member_position($member,$aln);
  Description: Obtain the member position for a given sitewise_omega value
  Returntype : integer
  Exceptions : return undef if member not in the alignment or aln_position not in member
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::SitewiseOmega::new_fast ( )
  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 :
  Exceptions : none
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::SitewiseOmega::node_id ( )
  Arg [1]    : (opt) integer
  Example    : $sitewise_dnds->node_id(1);
  Description: Getter/Setter for the node_id value
  Returnnode_id : integer. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Int Bio::EnsEMBL::Compara::SitewiseOmega::omega ( )
  Arg [1]    : (opt) integer
  Example    : $sitewise_dnds->omega(1);
  Description: Getter/Setter for the omega value
  Returntype : integer. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Float Bio::EnsEMBL::Compara::SitewiseOmega::omega_lower ( )
  Arg [1]    : (opt) float
  Example    : $sitewise_dnds->omega_lower(1);
  Description: Getter/Setter for the omega_lower value
  Returntype : float. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Float Bio::EnsEMBL::Compara::SitewiseOmega::omega_upper ( )
  Arg [1]    : (opt) float
  Example    : $sitewise_dnds->omega_upper(1);
  Description: Getter/Setter for the omega_upper value
  Returntype : float. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Float Bio::EnsEMBL::Compara::SitewiseOmega::optimal ( )
  Arg [1]    : (opt) float
  Example    : $sitewise_dnds->optimal(1);
  Description: Getter/Setter for the optimal value
  Returntype : float. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Float Bio::EnsEMBL::Compara::SitewiseOmega::threshold_on_branch_ds ( )
  Arg [1]    : (opt) float
  Example    : $sitewise_dnds->threshold_on_branch_ds(1);
  Description: Getter/Setter for the threshold_on_branch_ds value
  Returntype : float. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::SitewiseOmega::tree_node_id ( )
  Arg [1]    : (opt) integer
  Example    : $sitewise_dnds->tree_node_id(1);
  Description: Getter/Setter for the tree_node_id value
  Returntree_node_id : integer. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Int Bio::EnsEMBL::Compara::SitewiseOmega::type ( )
  Arg [1]    : (opt) integer
  Example    : $sitewise_dnds->type(1);
  Description: Getter/Setter for the type value
  Returntype : integer. Return 1 if value not defined
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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The documentation for this class was generated from the following file: