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Bio::EnsEMBL::Compara::PeptideAlignFeature Class Reference

List of all members.


Class Summary

Synopsis

      # Get an $homology object somehow

      # For Homology PeptideAlignFeatures, you normally get 2 pafs,
      # one for each member used alternatively as query and database
      # (hit) in the blast run

      my $pafs = $homology-\>get_all_PeptideAlignFeature;

      foreach my $paf (@{$pafs}) {
        print $paf-\>query_member-\>stable_id," ",$self-\>hit_member-\>stable_id," ",$paf-\>evalue,"\n";
      }

      # Other stuff in the object:
      # $paf-\>qstart
      # $paf-\>qend
      # $paf-\>hstart
      # $paf-\>hend
      # $paf-\>score
      # $paf-\>alignment_length
      # $paf-\>identical_matches
      # $paf-\>perc_ident
      # $paf-\>positive_matches
      # $paf-\>perc_pos
      # $paf-\>hit_rank
      # $paf-\>cigar_line

Description

 

Definition at line 40 of file PeptideAlignFeature.pm.

Available Methods

public alignment_length ()
public analysis ()
public cigar_line ()
public compact_cigar_line ()
public create_homology ()
public dbID ()
public display_short ()
public evalue ()
public get_description ()
public String hash_key ()
public hend ()
public hit_genome_db_id ()
public hit_member ()
public hit_member_id ()
public hit_rank ()
public hlength ()
public hstart ()
public identical_matches ()
public new ()
public perc_ident ()
public perc_pos ()
public positive_matches ()
public qend ()
public qlength ()
public qstart ()
public query_genome_db_id ()
public query_member ()
public query_member_id ()
public rhit_dbID ()
public score ()

Method Documentation

public Bio::EnsEMBL::Compara::PeptideAlignFeature::alignment_length ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::analysis ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::cigar_line ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::compact_cigar_line ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::create_homology ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::dbID ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::display_short ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::evalue ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::get_description ( )

Undocumented method

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public String Bio::EnsEMBL::Compara::PeptideAlignFeature::hash_key ( )
  Args       : none
  Example    : $somehash->{$paf->hash_key} = $someValue;
  Description: used for keeping track of known/stored gene/gene relationships
  Returntype : string $key
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hend ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hit_genome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hit_member ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hit_member_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hit_rank ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hlength ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::hstart ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::identical_matches ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::new ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::perc_ident ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::perc_pos ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::positive_matches ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::qend ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::qlength ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::qstart ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::query_genome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::query_member ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::query_member_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::rhit_dbID ( )

Undocumented method

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public Bio::EnsEMBL::Compara::PeptideAlignFeature::score ( )

Undocumented method

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