Class: Ensembl::Core::ProteinAlignFeature

Inherits:

DBConnection

• Object
• ActiveRecord::Base
• DBRegistry::Base
• DBConnection
• Ensembl::Core::ProteinAlignFeature

Includes:

Sliceable

Defined in:

lib/bio-ensembl/core/activerecord.rb

Overview

The ProteinAlignFeature class provides an interface to the protein_align_feature table. This table contains sequence similarity mappings against a SeqRegion.

This class uses ActiveRecord to access data in the Ensembl database. See the general documentation of the Ensembl module for more information on what this means and what methods are available.

This class includes the mixin Sliceable, which means that it is mapped to a SeqRegion object and a Slice can be created for objects of this class. See Sliceable and Slice for more information.

Examples:

uniprot_scan = Analysis.find_by_logic_name('Uniprot')
uniprot_scan.protein_align_features.each do |hit|
puts hit.seq_region.name + "\t" + hit.hit_name + "\t" + hit.cigar_line
end

Method Summary

Methods included from Sliceable

#length, #project, #seq, #slice, #start, #stop, #strand, #transform

Methods inherited from DBConnection

connect, ensemblgenomes_connect

Methods inherited from DBRegistry::Base

generic_connect, get_info, get_name_from_db