/ 
Bio-EnsEMBL-112.0_54
River stage zero No dependents
/ Bio::EnsEMBL::ProteinFeature

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::ProteinFeature

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.

METHODS

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

strand

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

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

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

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

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

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

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

_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

_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