Inheritance diagram for Bio::EnsEMBL::DnaPepAlignFeature:

Public Member Functions
protected Int	_hit_unit ()

protected Int	_query_unit ()

Public Member Functions inherited from Bio::EnsEMBL::BaseAlignFeature
public Bio::EnsEMBL::BaseAlignFeature	new ()

public String	cigar_string ()

public String	align_type ()

public Int	alignment_length ()

protected Int	_ensembl_cigar_alignment_length ()

public List	ungapped_features ()

public Int	strands_reversed ()

public void	reverse_complement ()

protected void	_ensembl_reverse_complement ()

public Bio::EnsEMBL::BaseAlignFeature	transform ()

protected List	_parse_ensembl_cigar ()

protected	_parse_cigar ()

protected void	_parse_features ()

protected	_parse_ensembl_features ()

protected Int	_hit_unit ()

protected Int	_query_unit ()

protected Int	_mdtag_alignment_length ()

protected Array	_get_mdz_chunks ()

protected Array	_get_mdz_alignment_length ()

protected String	_get_mdz_chunk_type ()

protected Array	_mdz_alignment_string ()

Public Member Functions inherited from Bio::EnsEMBL::FeaturePair
public Bio::EnsEMBL::FeaturePair	new ()

public String	hseqname ()

public Int	hstart ()

public Int	hend ()

public	hstrand ()

public Bio::EnsEMBL::Slice	hslice ()

public String	hseq_region_name ()

public Boolean	hseq_region_strand ()

public Int	hseq_region_start ()

public Int	hseq_region_end ()

public Float	score ()

public Float	percent_id ()

public String	species ()

public String	hspecies ()

public String	coverage ()

public String	hcoverage ()

public String	external_db_id ()

public String	db_name ()

public String	db_display_name ()

public Float	p_value ()

public String	hdescription ()

public String	display_id ()

public Int	identical_matches ()

public Int	positive_matches ()

public Int	group_id ()

public Int	level_id ()

public void	invert ()

public	extra_data ()

public	type ()

Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()

public Int	start ()

public Int	end ()

public Int	strand ()

public void	move ()

public Int	length ()

public Bio::EnsEMBL::Analysis	analysis ()

public Bio::EnsEMBL::Slice	slice ()

public Boolean Or Undef	equals ()

public Bio::EnsEMBL::Feature	transform ()

public Bio::EnsEMBL::Feature	transfer ()

public Listref	project_to_slice ()

public Listref	project ()

public String	seqname ()

public String	display_id ()

public String	version ()

public Bio::EnsEMBL::Slice	feature_Slice ()

public String	seq_region_name ()

public Int	seq_region_length ()

public Boolean	seq_region_strand ()

public Int	seq_region_start ()

public Int	seq_region_end ()

public String	coord_system_name ()

public String	seq ()

public Listref	get_all_alt_locations ()

public Boolean	overlaps ()

public Boolean	overlaps_local ()

public List	get_overlapping_Genes ()

public Bio::EnsEMBL::Gene	get_nearest_Gene ()

public String	feature_so_acc ()

public String	feature_so_term ()

public Hashref	summary_as_hash ()

public String	species ()

public	sub_SeqFeature ()

public	add_sub_SeqFeature ()

public	flush_sub_SeqFeature ()

Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()

public Instance	new_fast ()

public Int	dbID ()

public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()

public Boolean	is_stored ()

public	get_all_DAS_Features ()

Detailed Description

Synopsis

See BaseAlignFeature

Definition at line 12 of file DnaPepAlignFeature.pm.

Member Function Documentation

◆ _hit_unit()

protected Int Bio::EnsEMBL::DnaPepAlignFeature::_hit_unit ( )

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method.  Returns
               1 as the 'unit' used for the hit sequence. 
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable

Code:

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◆ _query_unit()

protected Int Bio::EnsEMBL::DnaPepAlignFeature::_query_unit ( )

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method.  Returns
               3 as the 'unit' used for the query sequence. 
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable