Bio::EnsEMBL::ProteinFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::ProteinFeature:

Public Member Functions
public Bio::EnsEMBL::FeaturePair	new ()
public Int	strand ()
public String	idesc ()
public String	ilabel ()
public String	interpro_ac ()
public String	translation_id ()
public	external_data ()
public Hashref	summary_as_hash ()
public Array	alignment_strings ()
public	transform ()
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

my $feature = Bio::EnsEMBL::ProteinFeature->new(
  -start    => $start,
  -end      => $end,
  -hstart   => $hit_start,
  -hend     => $hit_end,
  -hseqname => $hit_name
);

Description

ProteinFeature objects represent domains or other features of interest
on a peptide sequence.

Definition at line 24 of file ProteinFeature.pm.

Member Function Documentation

_hit_unit()

protected Int Bio::EnsEMBL::ProteinFeature::_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:

_query_unit()

protected Int Bio::EnsEMBL::ProteinFeature::_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

Code:

alignment_strings()

public Array Bio::EnsEMBL::ProteinFeature::alignment_strings

(

)

  Arg [1]    : list of string $flags
  Example    :

$pf->alignment_strings

  Description: Allows to rebuild the alignment string of both the query and target sequence
               using the sequence from translation object and
               MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer:  SAM/BAM specification)
               eg: MD:Z:96^RHKTDSFVGLMGKRALNS0V14
  Returntype : array reference containing 2 strings
               the first corresponds to seq
               the second corresponds to hseq
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

external_data()

public Bio::EnsEMBL::ProteinFeature::external_data

(

)

Undocumented method

Code:

idesc()

public String Bio::EnsEMBL::ProteinFeature::idesc

(

)

  Arg [1]    : (optional) string The interpro description
  Example    :

print $protein_feature->idesc();

  Description: Getter/Setter for the interpro description of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

ilabel()

public String Bio::EnsEMBL::ProteinFeature::ilabel

(

)

  Arg [1]    : (optional) string The interpro label
  Example    :

print $protein_feature->ilabel();

  Description: Getter/Setter for the interpro label of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

interpro_ac()

public String Bio::EnsEMBL::ProteinFeature::interpro_ac

(

)

  Arg [1]    : (optional) string The interpro accession
  Example    :

print $protein_feature->interpro_ac();

  Description: Getter/Setter for the interpro accession of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::FeaturePair Bio::EnsEMBL::ProteinFeature::new

(

)

  Arg [IDESC]           : (optional) string An interpro description
  Arg [INTERPRO_AC]     : (optional) string An interpro accession
  Arg [TRANSLATION_ID]  : (optional) integer A translation dbID
  Arg [...]             : named arguments to FeaturePair superclass
  Example    :

$pf =
  Bio::EnsEMBL::ProteinFeature->new( -IDESC       => $idesc,
                                     -INTERPRO_AC => $iac,
                                     @fp_args );

  Description: Instantiates a Bio::EnsEMBL::ProteinFeature
  Returntype : Bio::EnsEMBL::FeaturePair
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

strand()

public Int Bio::EnsEMBL::ProteinFeature::strand

(

)

  Arg [1]    : Ignored
  Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
             : the strand to be set.
  Returntype : int
  Status     : Stable

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::ProteinFeature::summary_as_hash

(

)

  Example       :

$protein_feature_summary = $protein_feature->summary_as_hash();

  Description   : Retrieves a textual summary of this Protein feature.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use
 

Code:

transform()

public Bio::EnsEMBL::ProteinFeature::transform

(

)

Undocumented method

Code:

translation_id()

public String Bio::EnsEMBL::ProteinFeature::translation_id

(

)

  Arg [1]    : (optional) integer The dbID of the translation
  Example    :

print $protein_feature->translation_id();

  Description: Getter/Setter for the translation dbID of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/ProteinFeature.pm